Starting phenix.real_space_refine on Thu Jul 31 14:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8va2_43085/07_2025/8va2_43085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8va2_43085/07_2025/8va2_43085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8va2_43085/07_2025/8va2_43085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8va2_43085/07_2025/8va2_43085.map" model { file = "/net/cci-nas-00/data/ceres_data/8va2_43085/07_2025/8va2_43085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8va2_43085/07_2025/8va2_43085.cif" } resolution = 4.5 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= 0.001 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 74 5.16 5 C 8470 2.51 5 N 2304 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13430 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3290 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 2 Chain: "b" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3290 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 2 Chain: "g" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3323 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 4 Chain: "h" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3405 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 20, 'TRANS': 404} Chain breaks: 3 Chain: "a" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.71, per 1000 atoms: 0.65 Number of scatterers: 13430 At special positions: 0 Unit cell: (113.52, 110.88, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 10 15.00 Mg 2 11.99 O 2570 8.00 N 2304 7.00 C 8470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 2.0 seconds 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 13 sheets defined 53.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'a' and resid 10 through 28 Processing helix chain 'a' and resid 47 through 51 removed outlier: 3.841A pdb=" N THR a 51 " --> pdb=" O SER a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 80 Processing helix chain 'a' and resid 110 through 113 Processing helix chain 'a' and resid 114 through 129 removed outlier: 3.711A pdb=" N GLN a 128 " --> pdb=" O LYS a 124 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS a 129 " --> pdb=" O LEU a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 161 Processing helix chain 'a' and resid 182 through 198 removed outlier: 3.683A pdb=" N HIS a 197 " --> pdb=" O THR a 193 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 216 Processing helix chain 'a' and resid 223 through 244 removed outlier: 3.972A pdb=" N SER a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 260 removed outlier: 3.532A pdb=" N VAL a 260 " --> pdb=" O GLN a 256 " (cutoff:3.500A) Processing helix chain 'a' and resid 278 through 283 removed outlier: 3.866A pdb=" N TYR a 282 " --> pdb=" O GLU a 279 " (cutoff:3.500A) Processing helix chain 'a' and resid 287 through 297 Processing helix chain 'a' and resid 298 through 301 Processing helix chain 'a' and resid 324 through 338 removed outlier: 3.575A pdb=" N LYS a 338 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 382 through 402 removed outlier: 3.827A pdb=" N GLU a 386 " --> pdb=" O THR a 382 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS a 401 " --> pdb=" O LEU a 397 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG a 402 " --> pdb=" O MET a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 410 Processing helix chain 'a' and resid 414 through 436 removed outlier: 3.562A pdb=" N PHE a 418 " --> pdb=" O GLU a 414 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 29 Processing helix chain 'b' and resid 48 through 51 Processing helix chain 'b' and resid 71 through 81 removed outlier: 4.762A pdb=" N ILE b 75 " --> pdb=" O GLU b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 108 Processing helix chain 'b' and resid 110 through 129 removed outlier: 3.821A pdb=" N ILE b 114 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP b 116 " --> pdb=" O LYS b 112 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU b 117 " --> pdb=" O GLU b 113 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN b 128 " --> pdb=" O LYS b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 161 Processing helix chain 'b' and resid 182 through 195 Processing helix chain 'b' and resid 205 through 216 removed outlier: 3.580A pdb=" N ILE b 209 " --> pdb=" O ASP b 205 " (cutoff:3.500A) Processing helix chain 'b' and resid 223 through 244 removed outlier: 4.377A pdb=" N SER b 241 " --> pdb=" O SER b 237 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU b 242 " --> pdb=" O ILE b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 251 through 259 removed outlier: 3.625A pdb=" N LEU b 259 " --> pdb=" O PHE b 255 " (cutoff:3.500A) Processing helix chain 'b' and resid 277 through 282 removed outlier: 4.014A pdb=" N TYR b 282 " --> pdb=" O ALA b 278 " (cutoff:3.500A) Processing helix chain 'b' and resid 287 through 297 Processing helix chain 'b' and resid 324 through 338 removed outlier: 3.768A pdb=" N LYS b 338 " --> pdb=" O THR b 334 " (cutoff:3.500A) Processing helix chain 'b' and resid 382 through 402 removed outlier: 3.661A pdb=" N GLU b 386 " --> pdb=" O THR b 382 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS b 401 " --> pdb=" O LEU b 397 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 410 removed outlier: 4.254A pdb=" N GLY b 410 " --> pdb=" O HIS b 406 " (cutoff:3.500A) Processing helix chain 'b' and resid 414 through 437 Processing helix chain 'g' and resid 10 through 29 Processing helix chain 'g' and resid 71 through 78 Processing helix chain 'g' and resid 82 through 86 Processing helix chain 'g' and resid 103 through 114 Processing helix chain 'g' and resid 114 through 128 removed outlier: 3.588A pdb=" N ILE g 118 " --> pdb=" O ILE g 114 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 143 through 159 Processing helix chain 'g' and resid 183 through 198 removed outlier: 3.640A pdb=" N ASN g 187 " --> pdb=" O VAL g 183 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 217 Processing helix chain 'g' and resid 224 through 245 removed outlier: 4.998A pdb=" N THR g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU g 243 " --> pdb=" O SER g 239 " (cutoff:3.500A) Processing helix chain 'g' and resid 252 through 259 Processing helix chain 'g' and resid 289 through 297 removed outlier: 3.517A pdb=" N MET g 294 " --> pdb=" O VAL g 290 " (cutoff:3.500A) Processing helix chain 'g' and resid 329 through 344 Processing helix chain 'g' and resid 384 through 400 removed outlier: 3.732A pdb=" N PHE g 388 " --> pdb=" O ILE g 384 " (cutoff:3.500A) Processing helix chain 'g' and resid 407 through 411 Processing helix chain 'g' and resid 418 through 439 Processing helix chain 'h' and resid 11 through 29 Processing helix chain 'h' and resid 39 through 44 removed outlier: 3.879A pdb=" N GLU h 43 " --> pdb=" O PHE h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 47 through 51 removed outlier: 3.602A pdb=" N VAL h 50 " --> pdb=" O ARG h 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE h 51 " --> pdb=" O LYS h 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 47 through 51' Processing helix chain 'h' and resid 70 through 79 removed outlier: 4.667A pdb=" N ILE h 74 " --> pdb=" O GLU h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 86 Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'h' and resid 103 through 129 removed outlier: 5.832A pdb=" N GLU h 116 " --> pdb=" O GLU h 112 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER h 129 " --> pdb=" O GLU h 125 " (cutoff:3.500A) Processing helix chain 'h' and resid 143 through 161 Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.517A pdb=" N ASN h 187 " --> pdb=" O VAL h 183 " (cutoff:3.500A) Processing helix chain 'h' and resid 207 through 219 removed outlier: 3.571A pdb=" N HIS h 219 " --> pdb=" O THR h 215 " (cutoff:3.500A) Processing helix chain 'h' and resid 223 through 245 removed outlier: 3.642A pdb=" N GLN h 227 " --> pdb=" O PRO h 223 " (cutoff:3.500A) Processing helix chain 'h' and resid 252 through 259 Processing helix chain 'h' and resid 263 through 267 Processing helix chain 'h' and resid 280 through 285 removed outlier: 3.693A pdb=" N VAL h 285 " --> pdb=" O SER h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 289 through 299 removed outlier: 3.699A pdb=" N GLN h 299 " --> pdb=" O ARG h 295 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 303 Processing helix chain 'h' and resid 329 through 344 Processing helix chain 'h' and resid 384 through 402 removed outlier: 4.081A pdb=" N PHE h 388 " --> pdb=" O ILE h 384 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG h 401 " --> pdb=" O LYS h 397 " (cutoff:3.500A) Processing helix chain 'h' and resid 405 through 410 Processing helix chain 'h' and resid 411 through 416 removed outlier: 4.264A pdb=" N ASP h 416 " --> pdb=" O ASP h 412 " (cutoff:3.500A) Processing helix chain 'h' and resid 418 through 440 removed outlier: 4.094A pdb=" N THR h 439 " --> pdb=" O TYR h 435 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG h 440 " --> pdb=" O HIS h 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 65 through 68 removed outlier: 3.737A pdb=" N ILE a 5 " --> pdb=" O GLY a 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 53 through 55 removed outlier: 3.696A pdb=" N SER a 54 " --> pdb=" O VAL a 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 353 through 356 Processing sheet with id=AA4, first strand: chain 'b' and resid 65 through 66 removed outlier: 3.522A pdb=" N VAL b 66 " --> pdb=" O SER b 6 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE b 5 " --> pdb=" O GLY b 134 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS b 200 " --> pdb=" O LYS b 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'b' and resid 269 through 270 removed outlier: 3.629A pdb=" N SER b 379 " --> pdb=" O LEU b 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'g' and resid 64 through 66 removed outlier: 8.647A pdb=" N VAL g 65 " --> pdb=" O ILE g 5 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR g 7 " --> pdb=" O VAL g 65 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE g 6 " --> pdb=" O GLY g 134 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE g 135 " --> pdb=" O GLN g 167 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR g 169 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU g 137 " --> pdb=" O TYR g 169 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL g 171 " --> pdb=" O LEU g 137 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N HIS g 139 " --> pdb=" O VAL g 171 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL g 166 " --> pdb=" O CYS g 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 52 through 54 removed outlier: 3.517A pdb=" N TYR g 53 " --> pdb=" O ILE g 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 270 through 273 removed outlier: 6.575A pdb=" N ASN g 380 " --> pdb=" O ILE g 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 270 through 273 removed outlier: 4.000A pdb=" N LEU g 321 " --> pdb=" O MET g 378 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASN g 322 " --> pdb=" O ALA g 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 66 through 67 removed outlier: 7.866A pdb=" N LEU h 67 " --> pdb=" O THR h 7 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN h 9 " --> pdb=" O LEU h 67 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE h 6 " --> pdb=" O GLY h 134 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU h 10 " --> pdb=" O CYS h 138 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE h 135 " --> pdb=" O GLN h 167 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR h 169 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU h 137 " --> pdb=" O TYR h 169 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL h 171 " --> pdb=" O LEU h 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 357 through 361 removed outlier: 9.206A pdb=" N GLN h 357 " --> pdb=" O ILE h 318 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE h 320 " --> pdb=" O GLN h 357 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ALA h 359 " --> pdb=" O ILE h 320 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN h 322 " --> pdb=" O ALA h 359 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER h 361 " --> pdb=" O ASN h 322 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE h 324 " --> pdb=" O SER h 361 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA h 319 " --> pdb=" O ASN h 380 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER h 374 " --> pdb=" O GLN h 325 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1875 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: 4.64 Time building geometry restraints manager: 4.29 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: 4440 1.34 - 1.47: 3191 1.47 - 1.59: 5970 1.59 - 1.71: 4 1.71 - 1.83: 118 Bond restraints: 13723 Sorted by residual: bond pdb=" O5' GTP b 501 " pdb=" PA GTP b 501 " ideal model delta sigma weight residual 1.610 1.831 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" O5' GTP a 501 " pdb=" PA GTP a 501 " ideal model delta sigma weight residual 1.610 1.828 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" O5' GDP h 501 " pdb=" PA GDP h 501 " ideal model delta sigma weight residual 1.610 1.745 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" O5' GDP g 501 " pdb=" PA GDP g 501 " ideal model delta sigma weight residual 1.610 1.731 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" O3A GDP h 501 " pdb=" PB GDP h 501 " ideal model delta sigma weight residual 1.610 1.730 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 13718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 18530 4.03 - 8.06: 63 8.06 - 12.09: 27 12.09 - 16.12: 19 16.12 - 20.15: 3 Bond angle restraints: 18642 Sorted by residual: angle pdb=" PA GDP g 501 " pdb=" O3A GDP g 501 " pdb=" PB GDP g 501 " ideal model delta sigma weight residual 120.50 140.65 -20.15 3.00e+00 1.11e-01 4.51e+01 angle pdb=" PA GDP h 501 " pdb=" O3A GDP h 501 " pdb=" PB GDP h 501 " ideal model delta sigma weight residual 120.50 140.38 -19.88 3.00e+00 1.11e-01 4.39e+01 angle pdb=" O2B GTP b 501 " pdb=" PB GTP b 501 " pdb=" O3A GTP b 501 " ideal model delta sigma weight residual 109.50 92.63 16.87 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O2B GTP a 501 " pdb=" PB GTP a 501 " pdb=" O3A GTP a 501 " ideal model delta sigma weight residual 109.50 93.99 15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" O1A GTP a 501 " pdb=" PA GTP a 501 " pdb=" O5' GTP a 501 " ideal model delta sigma weight residual 108.20 93.51 14.69 3.00e+00 1.11e-01 2.40e+01 ... (remaining 18637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 8007 33.50 - 66.99: 178 66.99 - 100.49: 17 100.49 - 133.99: 5 133.99 - 167.48: 5 Dihedral angle restraints: 8212 sinusoidal: 3328 harmonic: 4884 Sorted by residual: dihedral pdb=" C8 GTP b 501 " pdb=" C1' GTP b 501 " pdb=" N9 GTP b 501 " pdb=" O4' GTP b 501 " ideal model delta sinusoidal sigma weight residual 104.59 -62.89 167.48 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP a 501 " pdb=" C1' GTP a 501 " pdb=" N9 GTP a 501 " pdb=" O4' GTP a 501 " ideal model delta sinusoidal sigma weight residual 104.59 -60.69 165.28 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O5' GTP a 501 " pdb=" O3A GTP a 501 " pdb=" PA GTP a 501 " pdb=" PB GTP a 501 " ideal model delta sinusoidal sigma weight residual 274.12 110.56 163.57 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 8209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1888 0.075 - 0.149: 179 0.149 - 0.224: 2 0.224 - 0.298: 5 0.298 - 0.373: 5 Chirality restraints: 2079 Sorted by residual: chirality pdb=" C2' GDP h 501 " pdb=" C3' GDP h 501 " pdb=" O2' GDP h 501 " pdb=" C1' GDP h 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.88 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C3' GTP b 501 " pdb=" C2' GTP b 501 " pdb=" C4' GTP b 501 " pdb=" O3' GTP b 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.84 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C3' GTP a 501 " pdb=" C2' GTP a 501 " pdb=" C4' GTP a 501 " pdb=" O3' GTP a 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.82 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 2076 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL b 324 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO b 325 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO b 325 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 325 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN g 16 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C GLN g 16 " 0.027 2.00e-02 2.50e+03 pdb=" O GLN g 16 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE g 17 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 229 " -0.118 9.50e-02 1.11e+02 5.35e-02 2.24e+00 pdb=" NE ARG b 229 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG b 229 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG b 229 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG b 229 " -0.000 2.00e-02 2.50e+03 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 166 2.47 - 3.08: 11301 3.08 - 3.69: 21644 3.69 - 4.29: 30287 4.29 - 4.90: 49037 Nonbonded interactions: 112435 Sorted by model distance: nonbonded pdb=" O2G GTP a 501 " pdb="MG MG a 502 " model vdw 1.868 2.170 nonbonded pdb=" O2B GTP a 501 " pdb="MG MG a 502 " model vdw 1.888 2.170 nonbonded pdb=" O2G GTP b 501 " pdb="MG MG b 502 " model vdw 1.890 2.170 nonbonded pdb=" O HIS g 436 " pdb=" OG1 THR g 439 " model vdw 2.043 3.040 nonbonded pdb=" O ARG a 214 " pdb=" NH1 ARG a 214 " model vdw 2.122 3.120 ... (remaining 112430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'g' selection = (chain 'h' and (resid 4 through 278 or resid 290 through 441 or resid 501)) } 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 group one per residue 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: 7.740 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.720 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.006 0.221 13723 Z= 0.290 Angle : 0.873 20.146 18642 Z= 0.360 Chirality : 0.046 0.373 2079 Planarity : 0.003 0.053 2403 Dihedral : 15.735 167.483 5058 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1647 helix: 1.20 (0.19), residues: 755 sheet: -1.82 (0.36), residues: 209 loop : -1.31 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 351 HIS 0.006 0.001 HIS a 28 PHE 0.016 0.001 PHE g 119 TYR 0.016 0.001 TYR b 399 ARG 0.012 0.000 ARG b 229 Details of bonding type rmsd hydrogen bonds : bond 0.15172 ( 647) hydrogen bonds : angle 6.57563 ( 1875) covalent geometry : bond 0.00584 (13723) covalent geometry : angle 0.87273 (18642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 4.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 203 MET cc_start: 0.8895 (mmp) cc_final: 0.7801 (mmp) REVERT: a 259 LEU cc_start: 0.9375 (mt) cc_final: 0.9155 (mt) REVERT: a 377 MET cc_start: 0.8759 (ttp) cc_final: 0.8540 (ttp) REVERT: b 152 LEU cc_start: 0.9639 (tp) cc_final: 0.9351 (tp) REVERT: b 176 GLN cc_start: 0.8675 (mm110) cc_final: 0.8466 (mm-40) REVERT: b 183 GLU cc_start: 0.8533 (mp0) cc_final: 0.8207 (mp0) REVERT: b 185 TYR cc_start: 0.7832 (m-10) cc_final: 0.7221 (m-10) REVERT: b 203 MET cc_start: 0.9493 (mmp) cc_final: 0.8607 (mmm) REVERT: b 217 LEU cc_start: 0.8593 (mt) cc_final: 0.8265 (mt) REVERT: b 313 MET cc_start: 0.7661 (mtt) cc_final: 0.7209 (mpp) REVERT: b 318 LEU cc_start: 0.9098 (mt) cc_final: 0.8718 (mt) REVERT: g 244 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8568 (mpp80) REVERT: g 270 MET cc_start: 0.8283 (ptp) cc_final: 0.7831 (pmm) REVERT: g 378 MET cc_start: 0.8896 (mpp) cc_final: 0.8653 (mpp) REVERT: g 388 PHE cc_start: 0.8925 (m-10) cc_final: 0.8649 (m-10) REVERT: g 397 LYS cc_start: 0.8700 (tttt) cc_final: 0.7995 (mmmt) REVERT: g 421 MET cc_start: 0.9023 (mtp) cc_final: 0.8722 (mtp) REVERT: h 15 ASN cc_start: 0.8452 (m110) cc_final: 0.8163 (m110) REVERT: h 20 GLU cc_start: 0.8352 (tp30) cc_final: 0.7989 (tp30) REVERT: h 154 LEU cc_start: 0.9075 (mt) cc_final: 0.8829 (mt) REVERT: h 270 MET cc_start: 0.7221 (ttt) cc_final: 0.6996 (ttt) REVERT: h 271 THR cc_start: 0.7637 (p) cc_final: 0.7194 (p) REVERT: h 321 LEU cc_start: 0.9117 (tp) cc_final: 0.8820 (tp) REVERT: h 429 GLN cc_start: 0.8845 (mt0) cc_final: 0.8608 (mt0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3042 time to fit residues: 141.5998 Evaluate side-chains 250 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 186 ASN a 233 GLN a 258 ASN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067466 restraints weight = 53383.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.069423 restraints weight = 31946.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070904 restraints weight = 21169.397| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13723 Z= 0.168 Angle : 0.626 7.213 18642 Z= 0.320 Chirality : 0.046 0.215 2079 Planarity : 0.004 0.053 2403 Dihedral : 10.920 179.856 1871 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.27 % Allowed : 6.62 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1647 helix: 1.18 (0.19), residues: 764 sheet: -1.84 (0.32), residues: 242 loop : -1.01 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 388 HIS 0.011 0.001 HIS h 29 PHE 0.021 0.002 PHE h 21 TYR 0.016 0.001 TYR g 395 ARG 0.005 0.001 ARG a 214 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 647) hydrogen bonds : angle 5.40838 ( 1875) covalent geometry : bond 0.00377 (13723) covalent geometry : angle 0.62579 (18642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 319 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 167 LEU cc_start: 0.9182 (mm) cc_final: 0.8872 (mm) REVERT: a 203 MET cc_start: 0.8975 (mmp) cc_final: 0.7776 (mmp) REVERT: a 254 ASP cc_start: 0.7624 (t70) cc_final: 0.7059 (t70) REVERT: a 337 THR cc_start: 0.8458 (p) cc_final: 0.8236 (p) REVERT: a 349 THR cc_start: 0.9250 (p) cc_final: 0.9033 (p) REVERT: b 185 TYR cc_start: 0.7781 (m-10) cc_final: 0.7336 (m-10) REVERT: b 203 MET cc_start: 0.9448 (mmp) cc_final: 0.8445 (mmm) REVERT: b 217 LEU cc_start: 0.8615 (mt) cc_final: 0.8278 (mt) REVERT: b 260 VAL cc_start: 0.8916 (t) cc_final: 0.8597 (m) REVERT: b 313 MET cc_start: 0.7526 (mtt) cc_final: 0.7215 (mpp) REVERT: b 377 MET cc_start: 0.8691 (tmm) cc_final: 0.8207 (tmm) REVERT: g 22 TRP cc_start: 0.8541 (m100) cc_final: 0.8229 (m100) REVERT: g 52 PHE cc_start: 0.8620 (m-80) cc_final: 0.8373 (m-80) REVERT: g 197 GLN cc_start: 0.9315 (mm-40) cc_final: 0.9067 (mm-40) REVERT: g 377 MET cc_start: 0.8422 (tmm) cc_final: 0.8057 (tmm) REVERT: g 392 CYS cc_start: 0.8511 (p) cc_final: 0.8258 (p) REVERT: g 397 LYS cc_start: 0.8753 (tttt) cc_final: 0.8328 (mmmt) REVERT: h 15 ASN cc_start: 0.8463 (m110) cc_final: 0.8041 (m110) REVERT: h 20 GLU cc_start: 0.8406 (tp30) cc_final: 0.8078 (tp30) REVERT: h 204 VAL cc_start: 0.9301 (t) cc_final: 0.9008 (t) REVERT: h 271 THR cc_start: 0.7869 (p) cc_final: 0.7354 (p) outliers start: 4 outliers final: 0 residues processed: 321 average time/residue: 0.3258 time to fit residues: 161.2578 Evaluate side-chains 243 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 11 GLN ** a 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 ASN a 233 GLN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 309 HIS ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 ASN ** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 167 GLN h 187 ASN h 302 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068042 restraints weight = 53004.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070020 restraints weight = 31285.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071521 restraints weight = 20482.345| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13723 Z= 0.144 Angle : 0.601 6.435 18642 Z= 0.307 Chirality : 0.045 0.232 2079 Planarity : 0.004 0.051 2403 Dihedral : 10.041 166.469 1871 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1647 helix: 1.18 (0.18), residues: 763 sheet: -1.68 (0.32), residues: 236 loop : -0.90 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 21 HIS 0.007 0.001 HIS h 29 PHE 0.018 0.001 PHE g 225 TYR 0.016 0.001 TYR b 172 ARG 0.004 0.000 ARG g 244 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 647) hydrogen bonds : angle 5.20765 ( 1875) covalent geometry : bond 0.00325 (13723) covalent geometry : angle 0.60100 (18642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 167 LEU cc_start: 0.9227 (mm) cc_final: 0.8888 (mm) REVERT: a 196 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6859 (mm-30) REVERT: a 203 MET cc_start: 0.8986 (mmp) cc_final: 0.7799 (mmp) REVERT: a 377 MET cc_start: 0.8675 (ttp) cc_final: 0.8402 (ttp) REVERT: b 152 LEU cc_start: 0.9723 (tp) cc_final: 0.9510 (tp) REVERT: b 185 TYR cc_start: 0.7766 (m-10) cc_final: 0.7313 (m-10) REVERT: b 203 MET cc_start: 0.9386 (mmp) cc_final: 0.8568 (mmm) REVERT: b 210 TYR cc_start: 0.8463 (m-80) cc_final: 0.7970 (m-80) REVERT: b 217 LEU cc_start: 0.8655 (mt) cc_final: 0.8351 (mt) REVERT: b 260 VAL cc_start: 0.8944 (t) cc_final: 0.8526 (p) REVERT: g 197 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8927 (mm-40) REVERT: g 198 ASN cc_start: 0.8027 (m-40) cc_final: 0.7462 (m-40) REVERT: g 253 LEU cc_start: 0.8735 (tp) cc_final: 0.8212 (tp) REVERT: g 335 LYS cc_start: 0.9371 (mmpt) cc_final: 0.9076 (mmmt) REVERT: g 392 CYS cc_start: 0.8469 (p) cc_final: 0.8214 (p) REVERT: g 397 LYS cc_start: 0.8565 (tttt) cc_final: 0.8208 (mmmt) REVERT: g 421 MET cc_start: 0.9016 (mtp) cc_final: 0.8719 (mtp) REVERT: h 15 ASN cc_start: 0.8616 (m110) cc_final: 0.8254 (m110) REVERT: h 20 GLU cc_start: 0.8478 (tp30) cc_final: 0.8106 (tp30) REVERT: h 271 THR cc_start: 0.7873 (p) cc_final: 0.7373 (p) outliers start: 2 outliers final: 0 residues processed: 317 average time/residue: 0.2337 time to fit residues: 112.0063 Evaluate side-chains 249 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 186 ASN a 233 GLN a 301 GLN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 216 ASN g 15 ASN g 175 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 302 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066425 restraints weight = 53608.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.068332 restraints weight = 31847.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069756 restraints weight = 21256.356| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 13723 Z= 0.210 Angle : 0.647 7.291 18642 Z= 0.332 Chirality : 0.046 0.276 2079 Planarity : 0.004 0.048 2403 Dihedral : 9.960 159.828 1871 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1647 helix: 0.99 (0.18), residues: 764 sheet: -1.64 (0.32), residues: 246 loop : -0.86 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 346 HIS 0.007 0.001 HIS h 29 PHE 0.019 0.002 PHE h 21 TYR 0.029 0.002 TYR g 169 ARG 0.006 0.001 ARG a 320 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 647) hydrogen bonds : angle 5.23416 ( 1875) covalent geometry : bond 0.00465 (13723) covalent geometry : angle 0.64682 (18642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 ASP cc_start: 0.6929 (m-30) cc_final: 0.6545 (m-30) REVERT: a 167 LEU cc_start: 0.9251 (mm) cc_final: 0.8971 (mm) REVERT: a 196 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6933 (mm-30) REVERT: a 203 MET cc_start: 0.8987 (mmp) cc_final: 0.7886 (mmp) REVERT: a 293 ASN cc_start: 0.9131 (t0) cc_final: 0.8909 (t0) REVERT: a 415 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7868 (mt-10) REVERT: b 152 LEU cc_start: 0.9716 (tp) cc_final: 0.9481 (tp) REVERT: b 185 TYR cc_start: 0.7743 (m-10) cc_final: 0.7290 (m-10) REVERT: b 210 TYR cc_start: 0.8527 (m-80) cc_final: 0.8101 (m-80) REVERT: b 217 LEU cc_start: 0.8586 (mt) cc_final: 0.8286 (mt) REVERT: b 260 VAL cc_start: 0.8922 (t) cc_final: 0.8458 (p) REVERT: b 290 GLU cc_start: 0.8758 (pt0) cc_final: 0.8518 (pt0) REVERT: b 313 MET cc_start: 0.7908 (mpp) cc_final: 0.7642 (mpp) REVERT: g 22 TRP cc_start: 0.8564 (m100) cc_final: 0.8147 (m100) REVERT: g 103 ASN cc_start: 0.7577 (m110) cc_final: 0.7241 (m110) REVERT: g 197 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8964 (mm-40) REVERT: g 335 LYS cc_start: 0.9434 (mmpt) cc_final: 0.9195 (mmmt) REVERT: g 392 CYS cc_start: 0.8407 (p) cc_final: 0.8160 (p) REVERT: g 397 LYS cc_start: 0.8702 (tttt) cc_final: 0.8278 (mmmt) REVERT: g 421 MET cc_start: 0.9051 (mtp) cc_final: 0.8798 (mtp) REVERT: h 15 ASN cc_start: 0.8334 (m110) cc_final: 0.7970 (m110) REVERT: h 20 GLU cc_start: 0.8392 (tp30) cc_final: 0.7867 (tp30) REVERT: h 271 THR cc_start: 0.7716 (p) cc_final: 0.7235 (p) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2226 time to fit residues: 102.1833 Evaluate side-chains 245 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 162 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 chunk 125 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 61 HIS ** a 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 ASN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 158 ASN ** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068939 restraints weight = 52947.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070960 restraints weight = 31292.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072433 restraints weight = 20673.004| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13723 Z= 0.127 Angle : 0.602 6.966 18642 Z= 0.305 Chirality : 0.045 0.223 2079 Planarity : 0.004 0.045 2403 Dihedral : 9.584 156.956 1871 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.07 % Allowed : 2.73 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1647 helix: 1.10 (0.19), residues: 769 sheet: -1.35 (0.34), residues: 225 loop : -0.81 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 21 HIS 0.007 0.001 HIS h 115 PHE 0.018 0.001 PHE h 21 TYR 0.012 0.001 TYR g 169 ARG 0.006 0.000 ARG b 308 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 647) hydrogen bonds : angle 5.03742 ( 1875) covalent geometry : bond 0.00281 (13723) covalent geometry : angle 0.60249 (18642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 ASP cc_start: 0.6709 (m-30) cc_final: 0.6303 (m-30) REVERT: a 103 TYR cc_start: 0.7201 (t80) cc_final: 0.6723 (t80) REVERT: a 167 LEU cc_start: 0.9085 (mm) cc_final: 0.8677 (mm) REVERT: a 186 ASN cc_start: 0.8606 (m-40) cc_final: 0.8205 (m110) REVERT: a 196 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6923 (mm-30) REVERT: a 280 LYS cc_start: 0.0051 (tptp) cc_final: -0.0393 (tptp) REVERT: b 77 GLU cc_start: 0.8957 (pp20) cc_final: 0.8739 (pp20) REVERT: b 127 ASP cc_start: 0.9131 (p0) cc_final: 0.8857 (p0) REVERT: b 152 LEU cc_start: 0.9731 (tp) cc_final: 0.9470 (tp) REVERT: b 185 TYR cc_start: 0.7600 (m-10) cc_final: 0.7248 (m-10) REVERT: b 210 TYR cc_start: 0.8503 (m-80) cc_final: 0.8043 (m-80) REVERT: b 217 LEU cc_start: 0.8537 (mt) cc_final: 0.8249 (mt) REVERT: b 260 VAL cc_start: 0.8956 (t) cc_final: 0.8569 (p) REVERT: b 313 MET cc_start: 0.7723 (mpp) cc_final: 0.7489 (mpp) REVERT: b 422 ARG cc_start: 0.8664 (tpt90) cc_final: 0.8461 (tmm160) REVERT: g 22 TRP cc_start: 0.8536 (m100) cc_final: 0.8036 (m100) REVERT: g 103 ASN cc_start: 0.7521 (m110) cc_final: 0.7267 (m110) REVERT: g 197 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8761 (mm-40) REVERT: g 253 LEU cc_start: 0.8904 (tp) cc_final: 0.8626 (tp) REVERT: g 335 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9168 (mmmt) REVERT: g 392 CYS cc_start: 0.8364 (p) cc_final: 0.8136 (p) REVERT: g 397 LYS cc_start: 0.8554 (tttt) cc_final: 0.8182 (mmmt) REVERT: g 421 MET cc_start: 0.8969 (mtp) cc_final: 0.8701 (mtp) REVERT: h 15 ASN cc_start: 0.8487 (m110) cc_final: 0.7976 (m110) REVERT: h 20 GLU cc_start: 0.8305 (tp30) cc_final: 0.7781 (tp30) REVERT: h 193 LYS cc_start: 0.9298 (tptp) cc_final: 0.8906 (tttm) REVERT: h 271 THR cc_start: 0.7552 (p) cc_final: 0.7050 (p) REVERT: h 279 ASP cc_start: 0.7588 (m-30) cc_final: 0.7138 (t0) REVERT: h 292 ASP cc_start: 0.9130 (p0) cc_final: 0.8858 (p0) outliers start: 1 outliers final: 1 residues processed: 331 average time/residue: 0.2292 time to fit residues: 113.5939 Evaluate side-chains 264 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 61 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 161 optimal weight: 0.0770 chunk 147 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 233 GLN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 ASN ** g 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068469 restraints weight = 53695.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070468 restraints weight = 31762.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071944 restraints weight = 21157.737| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13723 Z= 0.143 Angle : 0.614 7.738 18642 Z= 0.311 Chirality : 0.045 0.198 2079 Planarity : 0.004 0.043 2403 Dihedral : 9.476 156.900 1871 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1647 helix: 1.11 (0.19), residues: 769 sheet: -1.16 (0.34), residues: 236 loop : -0.70 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 21 HIS 0.006 0.001 HIS g 115 PHE 0.020 0.001 PHE h 21 TYR 0.016 0.001 TYR h 92 ARG 0.006 0.001 ARG a 121 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 647) hydrogen bonds : angle 5.01995 ( 1875) covalent geometry : bond 0.00322 (13723) covalent geometry : angle 0.61374 (18642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 ASP cc_start: 0.6766 (m-30) cc_final: 0.6249 (m-30) REVERT: a 280 LYS cc_start: 0.0423 (tptp) cc_final: -0.0062 (tptm) REVERT: a 302 MET cc_start: 0.8140 (mtm) cc_final: 0.7854 (mtm) REVERT: b 77 GLU cc_start: 0.8967 (pp20) cc_final: 0.8760 (pp20) REVERT: b 152 LEU cc_start: 0.9722 (tp) cc_final: 0.9443 (tp) REVERT: b 185 TYR cc_start: 0.7607 (m-10) cc_final: 0.7037 (m-10) REVERT: b 210 TYR cc_start: 0.8251 (m-80) cc_final: 0.7689 (m-80) REVERT: b 217 LEU cc_start: 0.8510 (mt) cc_final: 0.8228 (mt) REVERT: b 260 VAL cc_start: 0.8964 (t) cc_final: 0.8532 (p) REVERT: b 295 CYS cc_start: 0.9032 (m) cc_final: 0.8777 (m) REVERT: b 303 VAL cc_start: 0.8917 (m) cc_final: 0.8691 (t) REVERT: b 313 MET cc_start: 0.7709 (mpp) cc_final: 0.7462 (mpp) REVERT: b 422 ARG cc_start: 0.8633 (tpt90) cc_final: 0.8220 (tmm160) REVERT: g 22 TRP cc_start: 0.8544 (m100) cc_final: 0.8142 (m100) REVERT: g 197 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8809 (mm-40) REVERT: g 206 ASP cc_start: 0.7967 (t0) cc_final: 0.7762 (t0) REVERT: g 297 LEU cc_start: 0.8434 (mp) cc_final: 0.8120 (mp) REVERT: g 335 LYS cc_start: 0.9424 (mmpt) cc_final: 0.9208 (mmmt) REVERT: g 397 LYS cc_start: 0.8557 (tttt) cc_final: 0.8206 (mmmt) REVERT: g 421 MET cc_start: 0.8977 (mtp) cc_final: 0.8712 (mtp) REVERT: h 15 ASN cc_start: 0.8471 (m110) cc_final: 0.7996 (m110) REVERT: h 20 GLU cc_start: 0.8233 (tp30) cc_final: 0.7741 (tp30) REVERT: h 21 PHE cc_start: 0.8614 (t80) cc_final: 0.7657 (t80) REVERT: h 271 THR cc_start: 0.7496 (p) cc_final: 0.7091 (p) REVERT: h 279 ASP cc_start: 0.7562 (m-30) cc_final: 0.7135 (t0) REVERT: h 292 ASP cc_start: 0.9163 (p0) cc_final: 0.8881 (p0) REVERT: h 324 ILE cc_start: 0.9055 (mm) cc_final: 0.8836 (mm) REVERT: h 377 MET cc_start: 0.8618 (ppp) cc_final: 0.8333 (ppp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2239 time to fit residues: 106.1848 Evaluate side-chains 263 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 35 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 103 optimal weight: 0.0870 chunk 162 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 186 ASN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069919 restraints weight = 52655.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071962 restraints weight = 31543.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073300 restraints weight = 20926.632| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13723 Z= 0.118 Angle : 0.612 7.904 18642 Z= 0.307 Chirality : 0.045 0.219 2079 Planarity : 0.004 0.043 2403 Dihedral : 9.253 155.174 1871 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1647 helix: 1.13 (0.19), residues: 767 sheet: -1.04 (0.33), residues: 241 loop : -0.62 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 21 HIS 0.008 0.001 HIS h 115 PHE 0.020 0.001 PHE g 119 TYR 0.021 0.001 TYR g 169 ARG 0.004 0.000 ARG a 422 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 647) hydrogen bonds : angle 4.91148 ( 1875) covalent geometry : bond 0.00261 (13723) covalent geometry : angle 0.61208 (18642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 ASP cc_start: 0.6754 (m-30) cc_final: 0.6141 (m-30) REVERT: a 103 TYR cc_start: 0.7229 (t80) cc_final: 0.6606 (t80) REVERT: a 186 ASN cc_start: 0.8662 (m-40) cc_final: 0.8094 (m110) REVERT: a 280 LYS cc_start: 0.0365 (tptp) cc_final: -0.0217 (tptp) REVERT: a 377 MET cc_start: 0.8701 (ttp) cc_final: 0.8461 (ttp) REVERT: b 77 GLU cc_start: 0.8978 (pp20) cc_final: 0.8776 (pp20) REVERT: b 118 VAL cc_start: 0.9296 (t) cc_final: 0.8963 (p) REVERT: b 152 LEU cc_start: 0.9720 (tp) cc_final: 0.9449 (tp) REVERT: b 185 TYR cc_start: 0.7601 (m-10) cc_final: 0.7143 (m-10) REVERT: b 187 SER cc_start: 0.9151 (m) cc_final: 0.8849 (p) REVERT: b 210 TYR cc_start: 0.8220 (m-80) cc_final: 0.7668 (m-80) REVERT: b 217 LEU cc_start: 0.8468 (mt) cc_final: 0.8203 (mt) REVERT: b 260 VAL cc_start: 0.8985 (t) cc_final: 0.8619 (p) REVERT: b 313 MET cc_start: 0.7738 (mpp) cc_final: 0.7465 (mpp) REVERT: g 22 TRP cc_start: 0.8411 (m100) cc_final: 0.7915 (m100) REVERT: g 197 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8820 (mm-40) REVERT: g 234 THR cc_start: 0.8969 (m) cc_final: 0.8692 (m) REVERT: g 297 LEU cc_start: 0.8399 (mp) cc_final: 0.8082 (mp) REVERT: g 335 LYS cc_start: 0.9377 (mmpt) cc_final: 0.9152 (mmmt) REVERT: g 397 LYS cc_start: 0.8585 (tttt) cc_final: 0.7878 (mmmt) REVERT: g 421 MET cc_start: 0.8917 (mtp) cc_final: 0.8677 (mtp) REVERT: h 20 GLU cc_start: 0.8174 (tp30) cc_final: 0.7831 (tp30) REVERT: h 167 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8258 (mm110) REVERT: h 178 MET cc_start: 0.5043 (ttp) cc_final: 0.4770 (ttp) REVERT: h 279 ASP cc_start: 0.7551 (m-30) cc_final: 0.7123 (t0) REVERT: h 292 ASP cc_start: 0.9138 (p0) cc_final: 0.8851 (p0) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2294 time to fit residues: 115.4658 Evaluate side-chains 275 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 233 GLN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 HIS g 15 ASN ** g 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 103 ASN ** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 167 GLN h 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068055 restraints weight = 53437.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.070041 restraints weight = 32161.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071483 restraints weight = 21510.213| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13723 Z= 0.171 Angle : 0.655 9.292 18642 Z= 0.331 Chirality : 0.045 0.188 2079 Planarity : 0.004 0.043 2403 Dihedral : 9.235 156.046 1871 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1647 helix: 0.97 (0.19), residues: 770 sheet: -1.10 (0.33), residues: 241 loop : -0.61 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 21 HIS 0.007 0.001 HIS g 115 PHE 0.024 0.002 PHE h 21 TYR 0.039 0.002 TYR g 169 ARG 0.006 0.001 ARG a 121 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 647) hydrogen bonds : angle 5.14408 ( 1875) covalent geometry : bond 0.00378 (13723) covalent geometry : angle 0.65490 (18642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 ASP cc_start: 0.6791 (m-30) cc_final: 0.6178 (m-30) REVERT: a 280 LYS cc_start: 0.0922 (tptp) cc_final: 0.0379 (tptm) REVERT: b 152 LEU cc_start: 0.9740 (tp) cc_final: 0.9493 (tp) REVERT: b 183 GLU cc_start: 0.8550 (mp0) cc_final: 0.8125 (mp0) REVERT: b 185 TYR cc_start: 0.7617 (m-10) cc_final: 0.7269 (m-10) REVERT: b 187 SER cc_start: 0.9149 (m) cc_final: 0.8812 (p) REVERT: b 210 TYR cc_start: 0.8268 (m-80) cc_final: 0.7673 (m-80) REVERT: b 217 LEU cc_start: 0.8527 (mt) cc_final: 0.8262 (mt) REVERT: b 260 VAL cc_start: 0.9047 (t) cc_final: 0.8715 (m) REVERT: b 313 MET cc_start: 0.7738 (mpp) cc_final: 0.7521 (mpp) REVERT: g 236 MET cc_start: 0.8662 (mmm) cc_final: 0.7473 (mmm) REVERT: g 397 LYS cc_start: 0.8576 (tttt) cc_final: 0.7866 (mmmt) REVERT: g 421 MET cc_start: 0.8980 (mtp) cc_final: 0.8709 (mtp) REVERT: h 20 GLU cc_start: 0.8215 (tp30) cc_final: 0.7934 (tp30) REVERT: h 167 GLN cc_start: 0.8469 (mm110) cc_final: 0.8179 (mm-40) REVERT: h 271 THR cc_start: 0.7938 (p) cc_final: 0.7468 (p) REVERT: h 279 ASP cc_start: 0.7540 (m-30) cc_final: 0.7116 (t0) REVERT: h 292 ASP cc_start: 0.9147 (p0) cc_final: 0.8853 (p0) REVERT: h 322 ASN cc_start: 0.7548 (t0) cc_final: 0.7336 (t0) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2199 time to fit residues: 103.8536 Evaluate side-chains 244 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 119 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 186 ASN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 103 ASN g 197 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068301 restraints weight = 52802.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070264 restraints weight = 31807.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071734 restraints weight = 21388.148| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13723 Z= 0.163 Angle : 0.662 9.526 18642 Z= 0.336 Chirality : 0.046 0.392 2079 Planarity : 0.004 0.042 2403 Dihedral : 9.199 155.772 1871 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1647 helix: 0.83 (0.18), residues: 781 sheet: -1.00 (0.34), residues: 231 loop : -0.72 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 21 HIS 0.004 0.001 HIS h 29 PHE 0.020 0.002 PHE h 21 TYR 0.034 0.002 TYR g 169 ARG 0.005 0.001 ARG a 422 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 647) hydrogen bonds : angle 5.20480 ( 1875) covalent geometry : bond 0.00361 (13723) covalent geometry : angle 0.66200 (18642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 ASP cc_start: 0.6351 (m-30) cc_final: 0.5812 (m-30) REVERT: a 280 LYS cc_start: 0.0975 (tptp) cc_final: 0.0425 (tptm) REVERT: a 377 MET cc_start: 0.8714 (ttp) cc_final: 0.8434 (ttp) REVERT: b 152 LEU cc_start: 0.9735 (tp) cc_final: 0.9463 (tp) REVERT: b 183 GLU cc_start: 0.8576 (mp0) cc_final: 0.8121 (mp0) REVERT: b 185 TYR cc_start: 0.7708 (m-10) cc_final: 0.7362 (m-10) REVERT: b 187 SER cc_start: 0.9101 (m) cc_final: 0.8790 (p) REVERT: b 210 TYR cc_start: 0.8261 (m-80) cc_final: 0.7699 (m-80) REVERT: b 217 LEU cc_start: 0.8561 (mt) cc_final: 0.8282 (mt) REVERT: g 22 TRP cc_start: 0.8507 (m100) cc_final: 0.8185 (m100) REVERT: g 236 MET cc_start: 0.8667 (mmm) cc_final: 0.6932 (mmm) REVERT: g 397 LYS cc_start: 0.8606 (tttt) cc_final: 0.7903 (mmmt) REVERT: g 421 MET cc_start: 0.8954 (mtp) cc_final: 0.8727 (mtp) REVERT: h 20 GLU cc_start: 0.8175 (tp30) cc_final: 0.7898 (tp30) REVERT: h 167 GLN cc_start: 0.8501 (mm110) cc_final: 0.8263 (mm-40) REVERT: h 271 THR cc_start: 0.7940 (p) cc_final: 0.7464 (p) REVERT: h 279 ASP cc_start: 0.7491 (m-30) cc_final: 0.6887 (t0) REVERT: h 292 ASP cc_start: 0.9156 (p0) cc_final: 0.8883 (p0) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2312 time to fit residues: 107.4374 Evaluate side-chains 252 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 186 ASN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 HIS ** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 GLN g 197 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069182 restraints weight = 52945.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071191 restraints weight = 31685.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072641 restraints weight = 21259.274| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13723 Z= 0.146 Angle : 0.662 9.863 18642 Z= 0.336 Chirality : 0.046 0.356 2079 Planarity : 0.004 0.041 2403 Dihedral : 9.119 154.998 1871 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1647 helix: 0.85 (0.19), residues: 778 sheet: -1.14 (0.33), residues: 241 loop : -0.71 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP h 22 HIS 0.006 0.001 HIS g 115 PHE 0.024 0.002 PHE g 119 TYR 0.029 0.001 TYR g 169 ARG 0.005 0.000 ARG a 422 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 647) hydrogen bonds : angle 5.15302 ( 1875) covalent geometry : bond 0.00326 (13723) covalent geometry : angle 0.66245 (18642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 ASP cc_start: 0.6329 (m-30) cc_final: 0.5750 (m-30) REVERT: a 280 LYS cc_start: 0.0894 (tptp) cc_final: 0.0255 (tptp) REVERT: b 152 LEU cc_start: 0.9734 (tp) cc_final: 0.9441 (tp) REVERT: b 183 GLU cc_start: 0.8550 (mp0) cc_final: 0.8078 (mp0) REVERT: b 185 TYR cc_start: 0.7601 (m-10) cc_final: 0.7295 (m-10) REVERT: b 187 SER cc_start: 0.9096 (m) cc_final: 0.8724 (p) REVERT: b 210 TYR cc_start: 0.8263 (m-80) cc_final: 0.7706 (m-80) REVERT: b 217 LEU cc_start: 0.8523 (mt) cc_final: 0.8251 (mt) REVERT: b 313 MET cc_start: 0.7988 (mpp) cc_final: 0.7772 (mpp) REVERT: g 22 TRP cc_start: 0.8489 (m100) cc_final: 0.8125 (m100) REVERT: g 397 LYS cc_start: 0.8464 (tttt) cc_final: 0.7776 (mmmt) REVERT: g 421 MET cc_start: 0.8960 (mtp) cc_final: 0.8733 (mtp) REVERT: h 167 GLN cc_start: 0.8480 (mm110) cc_final: 0.8197 (mm110) REVERT: h 236 MET cc_start: 0.7923 (ttp) cc_final: 0.7710 (ttp) REVERT: h 271 THR cc_start: 0.7929 (p) cc_final: 0.7332 (p) REVERT: h 279 ASP cc_start: 0.7563 (m-30) cc_final: 0.6994 (t0) REVERT: h 292 ASP cc_start: 0.9137 (p0) cc_final: 0.8844 (p0) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2243 time to fit residues: 102.2434 Evaluate side-chains 254 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.0000 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 186 ASN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 GLN g 197 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068675 restraints weight = 53282.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070657 restraints weight = 32052.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.072131 restraints weight = 21486.508| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13723 Z= 0.156 Angle : 0.658 10.096 18642 Z= 0.334 Chirality : 0.046 0.356 2079 Planarity : 0.004 0.041 2403 Dihedral : 9.084 155.382 1871 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1647 helix: 0.84 (0.19), residues: 779 sheet: -1.02 (0.34), residues: 233 loop : -0.73 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 21 HIS 0.004 0.001 HIS h 29 PHE 0.028 0.002 PHE g 119 TYR 0.021 0.001 TYR g 169 ARG 0.006 0.001 ARG h 295 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 647) hydrogen bonds : angle 5.15438 ( 1875) covalent geometry : bond 0.00348 (13723) covalent geometry : angle 0.65775 (18642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4109.25 seconds wall clock time: 73 minutes 56.27 seconds (4436.27 seconds total)