Starting phenix.real_space_refine on Sat Oct 11 02:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbf_37423/10_2025/8wbf_37423_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbf_37423/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wbf_37423/10_2025/8wbf_37423_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbf_37423/10_2025/8wbf_37423_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wbf_37423/10_2025/8wbf_37423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbf_37423/10_2025/8wbf_37423.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.137 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.97, per 1000 atoms: 0.27 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: 0.93 Conformation dependent library (CDL) restraints added in 438.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 1.67 Time building geometry restraints manager: 1.24 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 130 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 130 through 352)) selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.800 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (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 ARG 0.003 0.000 ARG a 29 TYR 0.009 0.001 TYR A 331 PHE 0.010 0.001 PHE B 277 TRP 0.021 0.001 TRP A 150 HIS 0.006 0.001 HIS b 164 Details of bonding type rmsd covalent geometry : bond 0.00232 (11208) covalent geometry : angle 0.50857 (15192) SS BOND : bond 0.00168 ( 24) SS BOND : angle 0.82015 ( 48) hydrogen bonds : bond 0.22813 ( 263) hydrogen bonds : angle 9.38571 ( 678) *********************** 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 : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7828 (t0) cc_final: 0.7512 (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: 0.6771 time to fit residues: 159.2668 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.156188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119797 restraints weight = 11902.648| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.23 r_work: 0.3203 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 11232 Z= 0.228 Angle : 0.660 16.036 15240 Z= 0.351 Chirality : 0.047 0.237 1592 Planarity : 0.005 0.047 1956 Dihedral : 4.789 21.015 1486 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.85 % Allowed : 10.80 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.23), residues: 1352 helix: 1.69 (0.42), residues: 152 sheet: -1.62 (0.31), residues: 322 loop : -0.91 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 257 TYR 0.012 0.002 TYR A 122 PHE 0.013 0.002 PHE B 277 TRP 0.022 0.002 TRP a 232 HIS 0.009 0.002 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00570 (11208) covalent geometry : angle 0.65034 (15192) SS BOND : bond 0.00676 ( 24) SS BOND : angle 2.14366 ( 48) hydrogen bonds : bond 0.04882 ( 263) hydrogen bonds : angle 6.28832 ( 678) *********************** 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 194 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5920 (tm-30) cc_final: 0.5325 (mt-10) REVERT: A 85 GLN cc_start: 0.8008 (mt0) cc_final: 0.7251 (mm110) REVERT: A 157 ASP cc_start: 0.7824 (t0) cc_final: 0.7601 (t0) REVERT: A 220 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7167 (mpt) REVERT: A 263 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: A 339 LYS cc_start: 0.6649 (pttm) cc_final: 0.6418 (pmtt) REVERT: B 103 ARG cc_start: 0.7899 (ptt90) cc_final: 0.7495 (ptt180) REVERT: B 251 LEU cc_start: 0.8941 (mt) cc_final: 0.8698 (mt) REVERT: B 263 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: B 274 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: B 340 GLU cc_start: 0.7727 (tp30) cc_final: 0.7443 (tp30) REVERT: a 63 MET cc_start: 0.7959 (mmm) cc_final: 0.7435 (mpt) REVERT: a 64 GLU cc_start: 0.6876 (tt0) cc_final: 0.6661 (tt0) REVERT: a 74 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6234 (tt0) REVERT: a 224 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: a 258 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7462 (mt-10) REVERT: a 274 GLU cc_start: 0.8768 (tt0) cc_final: 0.8508 (tt0) REVERT: a 278 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6384 (pt0) REVERT: a 284 LYS cc_start: 0.7114 (mttt) cc_final: 0.6678 (mmmt) REVERT: a 326 LYS cc_start: 0.6687 (mmtp) cc_final: 0.6297 (ttpt) REVERT: b 11 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6675 (mmtt) REVERT: b 97 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7365 (mtt) outliers start: 46 outliers final: 22 residues processed: 177 average time/residue: 0.6277 time to fit residues: 119.1458 Evaluate side-chains 168 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 232 TRP 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 232 TRP 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 140 LEU 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 97 MET 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 100 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN 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 = 0.3771 r_free = 0.3771 target = 0.156500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120128 restraints weight = 11873.880| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.22 r_work: 0.3206 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11232 Z= 0.172 Angle : 0.671 23.134 15240 Z= 0.348 Chirality : 0.045 0.220 1592 Planarity : 0.004 0.044 1956 Dihedral : 4.797 23.090 1486 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.43 % Allowed : 13.90 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.23), residues: 1352 helix: 1.79 (0.42), residues: 152 sheet: -1.67 (0.31), residues: 316 loop : -0.98 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 69 TYR 0.011 0.001 TYR A 331 PHE 0.012 0.001 PHE B 277 TRP 0.024 0.001 TRP b 232 HIS 0.005 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00419 (11208) covalent geometry : angle 0.64707 (15192) SS BOND : bond 0.00678 ( 24) SS BOND : angle 3.21785 ( 48) hydrogen bonds : bond 0.04276 ( 263) hydrogen bonds : angle 5.90043 ( 678) *********************** 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: 41 poor density : 144 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5600 (tm-30) cc_final: 0.5172 (mt-10) REVERT: A 263 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: B 103 ARG cc_start: 0.7885 (ptt90) cc_final: 0.7485 (ptt180) REVERT: B 251 LEU cc_start: 0.8879 (mt) cc_final: 0.8636 (mt) REVERT: B 263 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: B 274 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: B 340 GLU cc_start: 0.7709 (tp30) cc_final: 0.7409 (tp30) REVERT: a 63 MET cc_start: 0.7911 (mmm) cc_final: 0.7453 (mpt) REVERT: a 64 GLU cc_start: 0.6924 (tt0) cc_final: 0.6673 (tt0) REVERT: a 74 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6184 (tt0) REVERT: a 224 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: a 258 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7433 (mt-10) REVERT: a 274 GLU cc_start: 0.8744 (tt0) cc_final: 0.8505 (tt0) REVERT: a 284 LYS cc_start: 0.7076 (mttt) cc_final: 0.6571 (mmmt) REVERT: b 63 MET cc_start: 0.7282 (mmt) cc_final: 0.6732 (mmt) outliers start: 41 outliers final: 22 residues processed: 170 average time/residue: 0.6124 time to fit residues: 111.6070 Evaluate side-chains 153 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET 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 232 TRP Chi-restraints excluded: chain A residue 234 ASP 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 139 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 232 TRP 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 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 98 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116107 restraints weight = 11911.261| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.25 r_work: 0.3157 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11232 Z= 0.250 Angle : 0.728 23.089 15240 Z= 0.379 Chirality : 0.048 0.242 1592 Planarity : 0.005 0.045 1956 Dihedral : 5.096 24.094 1486 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.19 % Allowed : 15.58 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.23), residues: 1352 helix: 1.76 (0.42), residues: 152 sheet: -1.84 (0.32), residues: 282 loop : -1.17 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 261 TYR 0.015 0.002 TYR A 122 PHE 0.011 0.002 PHE B 277 TRP 0.028 0.002 TRP B 232 HIS 0.007 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00620 (11208) covalent geometry : angle 0.70644 (15192) SS BOND : bond 0.00646 ( 24) SS BOND : angle 3.17923 ( 48) hydrogen bonds : bond 0.04598 ( 263) hydrogen bonds : angle 5.91210 ( 678) *********************** 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: 50 poor density : 132 time to evaluate : 0.372 Fit side-chains REVERT: A 15 CYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6023 (t) REVERT: A 263 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: B 103 ARG cc_start: 0.7986 (ptt90) cc_final: 0.7601 (ptt180) REVERT: B 251 LEU cc_start: 0.8891 (mt) cc_final: 0.8648 (mt) REVERT: B 263 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: B 274 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: B 340 GLU cc_start: 0.7789 (tp30) cc_final: 0.7450 (tp30) REVERT: a 63 MET cc_start: 0.7954 (mmm) cc_final: 0.7156 (mpt) REVERT: a 64 GLU cc_start: 0.7011 (tt0) cc_final: 0.6742 (tt0) REVERT: a 74 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6205 (tt0) REVERT: a 224 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: a 258 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7454 (mt-10) REVERT: a 274 GLU cc_start: 0.8824 (tt0) cc_final: 0.8610 (tt0) REVERT: a 278 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6392 (pt0) REVERT: a 284 LYS cc_start: 0.7074 (mttt) cc_final: 0.6618 (mmmt) REVERT: b 11 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6618 (mmtt) REVERT: b 63 MET cc_start: 0.7731 (mmt) cc_final: 0.6844 (mpp) REVERT: b 97 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7444 (mtt) outliers start: 50 outliers final: 27 residues processed: 166 average time/residue: 0.6237 time to fit residues: 110.9912 Evaluate side-chains 163 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain B residue 13 THR 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 232 TRP 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 140 LEU 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 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 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 263 GLN a 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120639 restraints weight = 11731.865| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.43 r_work: 0.3238 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11232 Z= 0.110 Angle : 0.589 17.794 15240 Z= 0.310 Chirality : 0.042 0.197 1592 Planarity : 0.004 0.040 1956 Dihedral : 4.546 22.579 1486 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.18 % Allowed : 17.76 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.23), residues: 1352 helix: 2.16 (0.42), residues: 152 sheet: -1.52 (0.31), residues: 308 loop : -0.97 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 69 TYR 0.014 0.001 TYR A 122 PHE 0.012 0.001 PHE B 277 TRP 0.018 0.001 TRP A 232 HIS 0.004 0.001 HIS a 164 Details of bonding type rmsd covalent geometry : bond 0.00257 (11208) covalent geometry : angle 0.56906 (15192) SS BOND : bond 0.00425 ( 24) SS BOND : angle 2.78817 ( 48) hydrogen bonds : bond 0.03293 ( 263) hydrogen bonds : angle 5.45667 ( 678) *********************** 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 186 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5960 (tm-30) cc_final: 0.5191 (tt0) REVERT: A 258 GLU cc_start: 0.7056 (pm20) cc_final: 0.6849 (pm20) REVERT: A 263 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: B 103 ARG cc_start: 0.7981 (ptt90) cc_final: 0.7600 (ptt180) REVERT: B 251 LEU cc_start: 0.8816 (mt) cc_final: 0.8574 (mt) REVERT: a 63 MET cc_start: 0.7945 (mmm) cc_final: 0.7241 (mpt) REVERT: a 74 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6273 (tt0) REVERT: a 224 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: a 258 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7549 (mt-10) REVERT: a 274 GLU cc_start: 0.8789 (tt0) cc_final: 0.8577 (tt0) REVERT: a 284 LYS cc_start: 0.7207 (mttt) cc_final: 0.6750 (mmmt) REVERT: b 178 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7093 (mm-30) outliers start: 38 outliers final: 18 residues processed: 174 average time/residue: 0.6176 time to fit residues: 115.5555 Evaluate side-chains 156 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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 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 67 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 263 GLN a 254 HIS a 255 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.158330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120754 restraints weight = 11830.277| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.32 r_work: 0.3232 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11232 Z= 0.112 Angle : 0.588 17.039 15240 Z= 0.310 Chirality : 0.042 0.157 1592 Planarity : 0.004 0.038 1956 Dihedral : 4.390 22.093 1486 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.69 % Allowed : 17.84 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.23), residues: 1352 helix: 2.32 (0.42), residues: 152 sheet: -1.42 (0.32), residues: 304 loop : -0.88 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 261 TYR 0.013 0.001 TYR A 122 PHE 0.011 0.001 PHE B 277 TRP 0.024 0.001 TRP B 232 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00265 (11208) covalent geometry : angle 0.56870 (15192) SS BOND : bond 0.00363 ( 24) SS BOND : angle 2.71675 ( 48) hydrogen bonds : bond 0.03174 ( 263) hydrogen bonds : angle 5.30520 ( 678) *********************** 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 184 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5640 (tm-30) cc_final: 0.5119 (tt0) REVERT: A 258 GLU cc_start: 0.7003 (pm20) cc_final: 0.6786 (pm20) REVERT: A 263 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: B 103 ARG cc_start: 0.7930 (ptt90) cc_final: 0.7502 (ptt180) REVERT: a 74 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6091 (tt0) REVERT: a 224 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: a 258 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7457 (mt-10) REVERT: a 274 GLU cc_start: 0.8736 (tt0) cc_final: 0.8529 (tt0) REVERT: a 284 LYS cc_start: 0.7028 (mttt) cc_final: 0.6498 (mmmt) REVERT: b 97 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7367 (mtt) REVERT: b 178 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: b 279 GLU cc_start: 0.7349 (pt0) cc_final: 0.6755 (pm20) REVERT: b 349 MET cc_start: 0.7277 (mmt) cc_final: 0.6965 (mmm) outliers start: 44 outliers final: 24 residues processed: 169 average time/residue: 0.6027 time to fit residues: 109.7667 Evaluate side-chains 162 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 75 LEU 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 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 a residue 13 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 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 178 GLU Chi-restraints excluded: chain b residue 209 THR 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 114 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS B 263 GLN 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 = 0.3784 r_free = 0.3784 target = 0.158236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123202 restraints weight = 11779.464| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.10 r_work: 0.3217 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11232 Z= 0.135 Angle : 0.616 17.884 15240 Z= 0.322 Chirality : 0.043 0.209 1592 Planarity : 0.004 0.037 1956 Dihedral : 4.473 22.356 1486 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.18 % Allowed : 19.18 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.24), residues: 1352 helix: 2.22 (0.42), residues: 154 sheet: -1.54 (0.31), residues: 310 loop : -0.83 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 69 TYR 0.011 0.001 TYR b 34 PHE 0.010 0.001 PHE B 277 TRP 0.024 0.001 TRP B 232 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00326 (11208) covalent geometry : angle 0.59600 (15192) SS BOND : bond 0.00427 ( 24) SS BOND : angle 2.81863 ( 48) hydrogen bonds : bond 0.03427 ( 263) hydrogen bonds : angle 5.33763 ( 678) *********************** 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: 38 poor density : 135 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5664 (tm-30) cc_final: 0.5176 (tt0) REVERT: A 85 GLN cc_start: 0.8075 (mt0) cc_final: 0.7420 (mm110) REVERT: A 263 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: B 103 ARG cc_start: 0.7955 (ptt90) cc_final: 0.7551 (ptt180) REVERT: a 63 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7366 (mpt) REVERT: a 74 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6191 (tt0) REVERT: a 97 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8014 (mpp) REVERT: a 224 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: a 258 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7456 (mt-10) REVERT: a 284 LYS cc_start: 0.7124 (mttt) cc_final: 0.6589 (mmmt) REVERT: b 40 ARG cc_start: 0.5996 (tmt170) cc_final: 0.5717 (ttp-170) REVERT: b 97 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7513 (mtt) REVERT: b 178 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7008 (mm-30) outliers start: 38 outliers final: 25 residues processed: 159 average time/residue: 0.6483 time to fit residues: 110.6859 Evaluate side-chains 159 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 263 GLN 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 a residue 13 THR Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 97 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 178 GLU Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 228 SER Chi-restraints excluded: chain b residue 287 VAL 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 51 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS B 263 GLN 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 = 0.3826 r_free = 0.3826 target = 0.162559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128294 restraints weight = 11765.224| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.93 r_work: 0.3305 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 11232 Z= 0.098 Angle : 0.568 15.242 15240 Z= 0.299 Chirality : 0.042 0.184 1592 Planarity : 0.003 0.034 1956 Dihedral : 4.188 20.667 1486 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.85 % Allowed : 20.10 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.24), residues: 1352 helix: 2.41 (0.42), residues: 154 sheet: -1.45 (0.31), residues: 308 loop : -0.67 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 261 TYR 0.010 0.001 TYR A 122 PHE 0.011 0.001 PHE B 277 TRP 0.011 0.001 TRP a 28 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00225 (11208) covalent geometry : angle 0.54938 (15192) SS BOND : bond 0.00381 ( 24) SS BOND : angle 2.61376 ( 48) hydrogen bonds : bond 0.02950 ( 263) hydrogen bonds : angle 5.13850 ( 678) *********************** 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 183 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7702 (tp) REVERT: A 85 GLN cc_start: 0.8116 (mt0) cc_final: 0.7561 (mm110) REVERT: B 103 ARG cc_start: 0.7958 (ptt90) cc_final: 0.7607 (ptt180) REVERT: a 63 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7541 (mpt) REVERT: a 74 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6337 (tt0) REVERT: a 224 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: a 258 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7566 (mt-10) REVERT: a 284 LYS cc_start: 0.7303 (mttt) cc_final: 0.6869 (mmmt) REVERT: b 40 ARG cc_start: 0.6105 (tmt170) cc_final: 0.5871 (ttp-170) REVERT: b 349 MET cc_start: 0.7386 (mmt) cc_final: 0.7065 (mmm) outliers start: 34 outliers final: 17 residues processed: 173 average time/residue: 0.6041 time to fit residues: 112.5380 Evaluate side-chains 153 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 88 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 51 GLU 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 56 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 117 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.159973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125316 restraints weight = 11775.069| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.93 r_work: 0.3267 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11232 Z= 0.126 Angle : 0.626 17.201 15240 Z= 0.326 Chirality : 0.043 0.237 1592 Planarity : 0.004 0.040 1956 Dihedral : 4.312 21.812 1486 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.43 % Allowed : 20.69 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.24), residues: 1352 helix: 2.38 (0.42), residues: 154 sheet: -1.43 (0.32), residues: 306 loop : -0.69 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 261 TYR 0.009 0.001 TYR A 122 PHE 0.010 0.001 PHE B 277 TRP 0.023 0.001 TRP B 232 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00301 (11208) covalent geometry : angle 0.60047 (15192) SS BOND : bond 0.00502 ( 24) SS BOND : angle 3.17886 ( 48) hydrogen bonds : bond 0.03302 ( 263) hydrogen bonds : angle 5.22756 ( 678) *********************** 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 161 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: A 85 GLN cc_start: 0.8132 (mt0) cc_final: 0.7585 (mm110) REVERT: B 103 ARG cc_start: 0.7989 (ptt90) cc_final: 0.7635 (ptt180) REVERT: B 128 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7303 (tttm) REVERT: a 63 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7439 (mpt) REVERT: a 74 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6404 (tt0) REVERT: a 224 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: a 258 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7590 (mt-10) REVERT: a 284 LYS cc_start: 0.7252 (mttt) cc_final: 0.6826 (mmmt) REVERT: b 40 ARG cc_start: 0.6099 (tmt170) cc_final: 0.5865 (ttp-170) REVERT: b 97 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: b 279 GLU cc_start: 0.7039 (pt0) cc_final: 0.6607 (pm20) outliers start: 29 outliers final: 19 residues processed: 152 average time/residue: 0.6278 time to fit residues: 102.5943 Evaluate side-chains 150 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR 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 287 VAL 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 70 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 124 optimal weight: 0.0570 chunk 63 optimal weight: 0.9980 overall best weight: 1.1502 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.160127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125349 restraints weight = 11783.042| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.93 r_work: 0.3266 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11232 Z= 0.123 Angle : 0.623 16.998 15240 Z= 0.325 Chirality : 0.043 0.235 1592 Planarity : 0.004 0.040 1956 Dihedral : 4.326 21.712 1486 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.43 % Allowed : 20.77 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.24), residues: 1352 helix: 2.36 (0.42), residues: 154 sheet: -1.47 (0.32), residues: 310 loop : -0.67 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 69 TYR 0.021 0.001 TYR A 122 PHE 0.010 0.001 PHE B 277 TRP 0.020 0.001 TRP B 232 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00292 (11208) covalent geometry : angle 0.59887 (15192) SS BOND : bond 0.00469 ( 24) SS BOND : angle 3.14209 ( 48) hydrogen bonds : bond 0.03253 ( 263) hydrogen bonds : angle 5.23579 ( 678) ********************** 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 159 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: A 85 GLN cc_start: 0.8126 (mt0) cc_final: 0.7584 (mm110) REVERT: B 103 ARG cc_start: 0.7983 (ptt90) cc_final: 0.7635 (ptt180) REVERT: B 128 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7308 (tttm) REVERT: a 63 MET cc_start: 0.7814 (mpt) cc_final: 0.7350 (mpt) REVERT: a 74 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6438 (tt0) REVERT: a 224 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: a 258 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7591 (mt-10) REVERT: a 284 LYS cc_start: 0.7268 (mttt) cc_final: 0.6875 (mmmt) REVERT: b 40 ARG cc_start: 0.6116 (tmt170) cc_final: 0.5881 (ttp-170) REVERT: b 63 MET cc_start: 0.8391 (mpp) cc_final: 0.8181 (mmt) outliers start: 29 outliers final: 22 residues processed: 150 average time/residue: 0.6042 time to fit residues: 97.6653 Evaluate side-chains 154 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR 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 51 GLU Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 287 VAL 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 66 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 0.0270 chunk 101 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS B 263 GLN a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128438 restraints weight = 11775.277| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.89 r_work: 0.3324 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11232 Z= 0.100 Angle : 0.590 15.569 15240 Z= 0.309 Chirality : 0.042 0.223 1592 Planarity : 0.004 0.039 1956 Dihedral : 4.130 20.446 1486 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.26 % Allowed : 21.27 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.24), residues: 1352 helix: 2.47 (0.42), residues: 154 sheet: -1.43 (0.32), residues: 310 loop : -0.63 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 69 TYR 0.017 0.001 TYR A 122 PHE 0.010 0.001 PHE B 277 TRP 0.012 0.001 TRP B 232 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00227 (11208) covalent geometry : angle 0.56686 (15192) SS BOND : bond 0.00447 ( 24) SS BOND : angle 2.96267 ( 48) hydrogen bonds : bond 0.02983 ( 263) hydrogen bonds : angle 5.11612 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.09 seconds wall clock time: 73 minutes 35.50 seconds (4415.50 seconds total)