Starting phenix.real_space_refine on Sat Jul 20 12:33:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbf_37423/07_2024/8wbf_37423_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbf_37423/07_2024/8wbf_37423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbf_37423/07_2024/8wbf_37423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbf_37423/07_2024/8wbf_37423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbf_37423/07_2024/8wbf_37423_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbf_37423/07_2024/8wbf_37423_neut.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.137 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6852 2.51 5 N 1958 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10914 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2819 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2819 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "a" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "b" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 6.05, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 20 sheets defined 18.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 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: 2.74 Time building geometry restraints manager: 3.99 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: 99.80 - 106.69: 439 106.69 - 113.57: 6096 113.57 - 120.45: 3916 120.45 - 127.33: 4517 127.33 - 134.21: 224 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 2.440 nonbonded pdb=" O LEU a 231 " pdb=" OG SER a 252 " model vdw 2.228 2.440 nonbonded pdb=" OG SER A 297 " pdb=" O TYR A 331 " model vdw 2.233 2.440 nonbonded pdb=" O GLY A 266 " pdb=" OG SER A 348 " model vdw 2.240 2.440 nonbonded pdb=" O MET b 97 " pdb=" OG1 THR b 222 " model vdw 2.255 2.440 ... (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 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.920 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.410 ------------------------------------------------------------------------------- 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 11208 Z= 0.160 Angle : 0.509 4.870 15192 Z= 0.281 Chirality : 0.042 0.141 1592 Planarity : 0.003 0.027 1956 Dihedral : 13.353 87.141 4146 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1352 helix: 1.86 (0.43), residues: 148 sheet: -1.75 (0.31), residues: 302 loop : -0.82 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 150 HIS 0.006 0.001 HIS b 164 PHE 0.010 0.001 PHE B 277 TYR 0.009 0.001 TYR A 331 ARG 0.003 0.000 ARG a 29 *********************** 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 fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7828 (t0) cc_final: 0.7511 (t70) REVERT: A 261 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7473 (mtp180) REVERT: A 329 CYS cc_start: 0.7703 (t) cc_final: 0.7385 (t) REVERT: B 103 ARG cc_start: 0.7620 (ptt90) cc_final: 0.7222 (ptt180) REVERT: B 251 LEU cc_start: 0.8800 (mt) cc_final: 0.8536 (mt) REVERT: B 286 HIS cc_start: 0.6971 (m170) cc_final: 0.6650 (m-70) REVERT: a 7 ASP cc_start: 0.8067 (t0) cc_final: 0.7828 (t0) REVERT: a 74 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6390 (tt0) REVERT: a 82 ASN cc_start: 0.7339 (m110) cc_final: 0.7132 (m-40) REVERT: a 213 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8666 (tttt) REVERT: a 258 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7517 (mt-10) REVERT: a 274 GLU cc_start: 0.8772 (tt0) cc_final: 0.8469 (tt0) REVERT: a 284 LYS cc_start: 0.7260 (mttt) cc_final: 0.6882 (mmmt) REVERT: b 63 MET cc_start: 0.8131 (mmm) cc_final: 0.7777 (mmt) REVERT: b 69 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7534 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 1.2696 time to fit residues: 299.7653 Evaluate side-chains 150 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 0.0270 chunk 123 optimal weight: 0.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 11208 Z= 0.328 Angle : 0.609 15.300 15192 Z= 0.324 Chirality : 0.045 0.216 1592 Planarity : 0.004 0.047 1956 Dihedral : 4.661 19.487 1486 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.77 % Allowed : 10.13 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1352 helix: 1.72 (0.42), residues: 152 sheet: -1.52 (0.32), residues: 308 loop : -0.89 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 232 HIS 0.008 0.001 HIS a 254 PHE 0.014 0.002 PHE B 277 TYR 0.011 0.001 TYR b 34 ARG 0.007 0.001 ARG B 257 *********************** 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 197 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.394 Fit side-chains REVERT: A 263 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: B 103 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7301 (ptt180) REVERT: B 263 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: B 274 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: B 286 HIS cc_start: 0.7054 (m170) cc_final: 0.6718 (m-70) REVERT: a 63 MET cc_start: 0.7940 (mmm) cc_final: 0.7513 (mmt) REVERT: a 64 GLU cc_start: 0.6892 (tt0) cc_final: 0.6690 (tt0) REVERT: a 74 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6390 (tt0) REVERT: a 224 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: a 258 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7423 (mt-10) REVERT: a 274 GLU cc_start: 0.8695 (tt0) cc_final: 0.8405 (tt0) REVERT: a 284 LYS cc_start: 0.7277 (mttt) cc_final: 0.6925 (mmmt) REVERT: b 11 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6592 (mmtt) REVERT: b 63 MET cc_start: 0.8186 (mmm) cc_final: 0.7845 (mmt) outliers start: 45 outliers final: 24 residues processed: 177 average time/residue: 1.2477 time to fit residues: 238.5973 Evaluate side-chains 163 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 87 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 139 THR Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 232 TRP Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 254 HIS a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11208 Z= 0.168 Angle : 0.578 22.209 15192 Z= 0.301 Chirality : 0.042 0.193 1592 Planarity : 0.004 0.041 1956 Dihedral : 4.435 21.633 1486 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.43 % Allowed : 13.57 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1352 helix: 1.98 (0.42), residues: 152 sheet: -1.61 (0.31), residues: 316 loop : -0.84 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 232 HIS 0.004 0.001 HIS b 164 PHE 0.012 0.001 PHE B 277 TYR 0.008 0.001 TYR A 122 ARG 0.009 0.000 ARG b 261 *********************** 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 183 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.275 Fit side-chains REVERT: A 261 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7457 (mtp180) REVERT: A 263 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 103 ARG cc_start: 0.7650 (ptt90) cc_final: 0.7258 (ptt180) REVERT: B 274 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: B 286 HIS cc_start: 0.7051 (m170) cc_final: 0.6739 (m-70) REVERT: a 63 MET cc_start: 0.7893 (mmm) cc_final: 0.7450 (mmt) REVERT: a 74 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6341 (tt0) REVERT: a 224 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: a 258 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7467 (mt-10) REVERT: a 274 GLU cc_start: 0.8660 (tt0) cc_final: 0.8381 (tt0) REVERT: a 284 LYS cc_start: 0.7249 (mttt) cc_final: 0.6884 (mmmt) REVERT: b 63 MET cc_start: 0.8152 (mmm) cc_final: 0.7904 (mmt) outliers start: 41 outliers final: 21 residues processed: 167 average time/residue: 1.2524 time to fit residues: 225.9297 Evaluate side-chains 154 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 78 ILE Chi-restraints excluded: chain A residue 86 LEU 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 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 139 THR 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 232 TRP 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 122 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN B 344 ASN a 254 HIS b 147 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 11208 Z= 0.604 Angle : 0.802 23.794 15192 Z= 0.417 Chirality : 0.052 0.211 1592 Planarity : 0.006 0.055 1956 Dihedral : 5.383 25.602 1486 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 4.61 % Allowed : 15.91 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.23), residues: 1352 helix: 1.42 (0.42), residues: 152 sheet: -1.78 (0.32), residues: 292 loop : -1.25 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 232 HIS 0.008 0.002 HIS b 35 PHE 0.013 0.003 PHE a 323 TYR 0.030 0.003 TYR B 331 ARG 0.008 0.001 ARG b 261 *********************** 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 186 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 131 time to evaluate : 1.296 Fit side-chains REVERT: B 103 ARG cc_start: 0.7860 (ptt90) cc_final: 0.7400 (ptt180) REVERT: B 263 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: B 274 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: B 340 GLU cc_start: 0.7726 (tp30) cc_final: 0.7494 (tp30) REVERT: a 41 ARG cc_start: 0.6615 (mtp-110) cc_final: 0.6408 (ttm-80) REVERT: a 64 GLU cc_start: 0.7030 (tt0) cc_final: 0.6812 (tt0) REVERT: a 74 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6394 (tt0) REVERT: a 224 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: a 258 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7329 (mt-10) REVERT: a 274 GLU cc_start: 0.8668 (tt0) cc_final: 0.8429 (tt0) REVERT: a 278 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6521 (pt0) REVERT: a 284 LYS cc_start: 0.7197 (mttt) cc_final: 0.6797 (mmmt) REVERT: b 11 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6650 (mmtt) REVERT: b 63 MET cc_start: 0.8276 (mmm) cc_final: 0.8022 (mmt) REVERT: b 97 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7361 (mtt) REVERT: b 314 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6299 (ttt180) outliers start: 55 outliers final: 30 residues processed: 165 average time/residue: 1.2871 time to fit residues: 229.1961 Evaluate side-chains 161 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 239 SER 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 115 TRP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 251 LEU 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 106 VAL Chi-restraints excluded: chain a residue 139 THR 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 314 ARG 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 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 0 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 23 ASN B 131 ASN B 263 GLN a 254 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11208 Z= 0.174 Angle : 0.565 16.260 15192 Z= 0.298 Chirality : 0.042 0.165 1592 Planarity : 0.004 0.041 1956 Dihedral : 4.659 22.945 1486 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.27 % Allowed : 17.84 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1352 helix: 2.01 (0.42), residues: 152 sheet: -1.72 (0.32), residues: 282 loop : -1.05 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 232 HIS 0.004 0.001 HIS b 164 PHE 0.012 0.001 PHE B 277 TYR 0.020 0.001 TYR b 175 ARG 0.008 0.000 ARG b 69 *********************** 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 176 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: B 103 ARG cc_start: 0.7661 (ptt90) cc_final: 0.7254 (ptt180) REVERT: B 274 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: a 63 MET cc_start: 0.7338 (mmt) cc_final: 0.6950 (mpt) REVERT: a 64 GLU cc_start: 0.6899 (tt0) cc_final: 0.6680 (tt0) REVERT: a 74 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6359 (tt0) REVERT: a 224 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: a 258 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7335 (mt-10) REVERT: a 274 GLU cc_start: 0.8665 (tt0) cc_final: 0.8406 (tt0) REVERT: a 278 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6514 (pt0) REVERT: a 284 LYS cc_start: 0.7159 (mttt) cc_final: 0.6787 (mmmt) REVERT: b 97 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7162 (mtt) outliers start: 39 outliers final: 23 residues processed: 165 average time/residue: 1.2795 time to fit residues: 227.7671 Evaluate side-chains 152 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 139 THR Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 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 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 118 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 263 GLN a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11208 Z= 0.336 Angle : 0.654 18.989 15192 Z= 0.341 Chirality : 0.045 0.189 1592 Planarity : 0.005 0.050 1956 Dihedral : 4.885 24.093 1486 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.27 % Allowed : 17.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.23), residues: 1352 helix: 1.97 (0.42), residues: 152 sheet: -1.81 (0.32), residues: 288 loop : -1.09 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 232 HIS 0.006 0.001 HIS a 254 PHE 0.011 0.002 PHE B 277 TYR 0.019 0.002 TYR b 175 ARG 0.009 0.001 ARG b 261 *********************** 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 181 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 130 time to evaluate : 2.254 Fit side-chains revert: symmetry clash REVERT: B 103 ARG cc_start: 0.7809 (ptt90) cc_final: 0.7384 (ptt180) REVERT: B 263 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.7672 (mp-120) REVERT: B 274 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: a 63 MET cc_start: 0.7586 (mmt) cc_final: 0.6801 (mpt) REVERT: a 64 GLU cc_start: 0.6952 (tt0) cc_final: 0.6741 (tt0) REVERT: a 74 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6416 (tt0) REVERT: a 224 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: a 258 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7294 (mt-10) REVERT: a 274 GLU cc_start: 0.8680 (tt0) cc_final: 0.8439 (tt0) REVERT: a 278 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6670 (pt0) REVERT: a 284 LYS cc_start: 0.7112 (mttt) cc_final: 0.6736 (mmmt) REVERT: b 178 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6905 (mm-30) outliers start: 51 outliers final: 32 residues processed: 165 average time/residue: 1.2364 time to fit residues: 219.7933 Evaluate side-chains 163 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 75 LEU 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 B residue 15 CYS Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 139 THR Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 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 228 SER 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 14 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 263 GLN a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11208 Z= 0.334 Angle : 0.654 18.964 15192 Z= 0.342 Chirality : 0.045 0.193 1592 Planarity : 0.005 0.043 1956 Dihedral : 4.918 23.905 1486 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.10 % Allowed : 17.50 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1352 helix: 1.95 (0.42), residues: 152 sheet: -1.85 (0.32), residues: 288 loop : -1.12 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 232 HIS 0.005 0.001 HIS B 254 PHE 0.011 0.002 PHE a 323 TYR 0.019 0.002 TYR A 122 ARG 0.008 0.001 ARG b 69 *********************** 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 178 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 129 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: B 103 ARG cc_start: 0.7789 (ptt90) cc_final: 0.7373 (ptt180) REVERT: B 263 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7591 (mp-120) REVERT: B 274 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: B 340 GLU cc_start: 0.7679 (tp30) cc_final: 0.7386 (tp30) REVERT: a 63 MET cc_start: 0.7557 (mmt) cc_final: 0.6702 (mpt) REVERT: a 64 GLU cc_start: 0.6904 (tt0) cc_final: 0.6658 (tt0) REVERT: a 74 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6437 (tt0) REVERT: a 224 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: a 258 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7273 (mt-10) REVERT: a 274 GLU cc_start: 0.8678 (tt0) cc_final: 0.8451 (tt0) REVERT: a 278 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6670 (pt0) REVERT: a 284 LYS cc_start: 0.7144 (mttt) cc_final: 0.6709 (mmmt) REVERT: b 11 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6523 (mmtt) REVERT: b 178 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6902 (mm-30) outliers start: 49 outliers final: 36 residues processed: 162 average time/residue: 1.1934 time to fit residues: 209.5723 Evaluate side-chains 168 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 75 LEU 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 A residue 350 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 139 THR Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 131 ASN 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 78 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 263 GLN a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11208 Z= 0.280 Angle : 0.626 18.136 15192 Z= 0.327 Chirality : 0.044 0.191 1592 Planarity : 0.004 0.042 1956 Dihedral : 4.825 23.659 1486 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 4.19 % Allowed : 17.67 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1352 helix: 2.05 (0.42), residues: 152 sheet: -1.70 (0.32), residues: 282 loop : -1.11 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 28 HIS 0.005 0.001 HIS a 254 PHE 0.011 0.001 PHE B 277 TYR 0.017 0.001 TYR b 175 ARG 0.008 0.000 ARG b 261 *********************** 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 fitting. rotamer outliers: 50 poor density : 133 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: A 263 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: B 103 ARG cc_start: 0.7781 (ptt90) cc_final: 0.7367 (ptt180) REVERT: B 263 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7540 (mp-120) REVERT: B 274 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: B 340 GLU cc_start: 0.7647 (tp30) cc_final: 0.7434 (tp30) REVERT: a 64 GLU cc_start: 0.6904 (tt0) cc_final: 0.6690 (tt0) REVERT: a 74 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6423 (tt0) REVERT: a 224 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: a 258 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7302 (mt-10) REVERT: a 274 GLU cc_start: 0.8679 (tt0) cc_final: 0.8441 (tt0) REVERT: a 278 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6684 (pt0) REVERT: a 284 LYS cc_start: 0.7151 (mttt) cc_final: 0.6693 (mmmt) REVERT: b 11 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6560 (mmtt) REVERT: b 178 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: b 316 CYS cc_start: 0.6625 (m) cc_final: 0.6120 (m) REVERT: b 349 MET cc_start: 0.7153 (mmt) cc_final: 0.6926 (mmm) outliers start: 50 outliers final: 39 residues processed: 166 average time/residue: 1.2128 time to fit residues: 217.7297 Evaluate side-chains 173 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 78 ILE 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 A residue 350 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 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 106 VAL Chi-restraints excluded: chain a residue 139 THR Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 131 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.0020 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 0.0010 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 263 GLN a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 11208 Z= 0.163 Angle : 0.560 14.823 15192 Z= 0.294 Chirality : 0.042 0.168 1592 Planarity : 0.004 0.054 1956 Dihedral : 4.453 21.856 1486 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.52 % Allowed : 18.93 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1352 helix: 2.33 (0.42), residues: 152 sheet: -1.46 (0.32), residues: 288 loop : -0.97 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 115 HIS 0.004 0.001 HIS b 164 PHE 0.012 0.001 PHE B 277 TYR 0.017 0.001 TYR b 175 ARG 0.012 0.000 ARG b 347 *********************** 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 180 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 138 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 263 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: A 326 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8120 (ttmm) REVERT: B 103 ARG cc_start: 0.7699 (ptt90) cc_final: 0.7253 (ptt180) REVERT: B 263 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7659 (mp-120) REVERT: B 274 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: a 74 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6326 (tt0) REVERT: a 224 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: a 258 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7292 (mt-10) REVERT: a 274 GLU cc_start: 0.8645 (tt0) cc_final: 0.8390 (tt0) REVERT: a 278 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6663 (pt0) REVERT: a 284 LYS cc_start: 0.7060 (mttt) cc_final: 0.6762 (mmtp) REVERT: b 97 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6908 (mtt) REVERT: b 178 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6878 (mm-30) outliers start: 42 outliers final: 25 residues processed: 168 average time/residue: 1.2341 time to fit residues: 223.5005 Evaluate side-chains 163 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 78 ILE 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 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 139 THR Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 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 131 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 263 GLN a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11208 Z= 0.280 Angle : 0.653 19.792 15192 Z= 0.340 Chirality : 0.044 0.212 1592 Planarity : 0.004 0.067 1956 Dihedral : 4.683 23.379 1486 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.27 % Allowed : 19.51 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1352 helix: 2.18 (0.42), residues: 154 sheet: -1.67 (0.33), residues: 266 loop : -1.03 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 28 HIS 0.005 0.001 HIS a 254 PHE 0.010 0.001 PHE B 277 TYR 0.016 0.001 TYR b 175 ARG 0.013 0.001 ARG b 347 ********************** 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 176 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: A 326 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8145 (ttmm) REVERT: B 103 ARG cc_start: 0.7775 (ptt90) cc_final: 0.7325 (ptt180) REVERT: B 274 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: B 289 GLU cc_start: 0.7619 (tp30) cc_final: 0.7254 (tp30) REVERT: B 340 GLU cc_start: 0.7612 (tp30) cc_final: 0.7344 (tp30) REVERT: a 64 GLU cc_start: 0.6900 (tt0) cc_final: 0.6641 (tt0) REVERT: a 74 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6341 (tt0) REVERT: a 224 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: a 258 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7306 (mt-10) REVERT: a 274 GLU cc_start: 0.8661 (tt0) cc_final: 0.8426 (tt0) REVERT: a 278 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6748 (pt0) REVERT: a 284 LYS cc_start: 0.7129 (mttt) cc_final: 0.6665 (mmmt) REVERT: b 178 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6887 (mm-30) REVERT: b 279 GLU cc_start: 0.7118 (pt0) cc_final: 0.6815 (tt0) outliers start: 39 outliers final: 29 residues processed: 162 average time/residue: 1.2361 time to fit residues: 215.8595 Evaluate side-chains 163 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 A residue 84 VAL Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 139 THR Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain 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 131 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN a 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120450 restraints weight = 11685.664| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.28 r_work: 0.3217 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11208 Z= 0.195 Angle : 0.607 19.136 15192 Z= 0.317 Chirality : 0.043 0.213 1592 Planarity : 0.004 0.064 1956 Dihedral : 4.500 22.332 1486 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.02 % Allowed : 19.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1352 helix: 2.30 (0.42), residues: 154 sheet: -1.43 (0.32), residues: 284 loop : -0.96 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 28 HIS 0.004 0.001 HIS a 254 PHE 0.011 0.001 PHE B 277 TYR 0.016 0.001 TYR b 175 ARG 0.014 0.000 ARG b 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4303.83 seconds wall clock time: 76 minutes 27.22 seconds (4587.22 seconds total)