Starting phenix.real_space_refine on Sat Oct 12 23:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va2_43085/10_2024/8va2_43085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va2_43085/10_2024/8va2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va2_43085/10_2024/8va2_43085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va2_43085/10_2024/8va2_43085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va2_43085/10_2024/8va2_43085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8va2_43085/10_2024/8va2_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-5477/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: 8.69, 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: 3.62 Conformation dependent library (CDL) restraints added in 1.8 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: 1.50 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: 4.21 Time building geometry restraints manager: 4.19 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: 4.460 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.580 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- 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= 0.415 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.479 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: 0.2344 time to fit residues: 108.5004 Evaluate side-chains 250 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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= 0.252 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 319 time to evaluate : 1.648 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: 0.9142 (mm) cc_final: 0.8837 (mm) REVERT: a 203 MET cc_start: 0.8960 (mmp) cc_final: 0.7760 (mmp) REVERT: a 254 ASP cc_start: 0.7551 (t70) cc_final: 0.7028 (t70) REVERT: a 337 THR cc_start: 0.8442 (p) cc_final: 0.8211 (p) REVERT: a 349 THR cc_start: 0.9235 (p) cc_final: 0.8998 (p) REVERT: b 185 TYR cc_start: 0.7740 (m-10) cc_final: 0.7299 (m-10) REVERT: b 203 MET cc_start: 0.9452 (mmp) cc_final: 0.8449 (mmm) REVERT: b 217 LEU cc_start: 0.8644 (mt) cc_final: 0.8294 (mt) REVERT: b 254 ASP cc_start: 0.8688 (m-30) cc_final: 0.8468 (m-30) REVERT: b 260 VAL cc_start: 0.8911 (t) cc_final: 0.8605 (m) REVERT: b 301 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8397 (pt0) REVERT: b 313 MET cc_start: 0.7371 (mtt) cc_final: 0.7109 (mpp) REVERT: b 377 MET cc_start: 0.8729 (tmm) cc_final: 0.8205 (tmm) REVERT: g 22 TRP cc_start: 0.8564 (m100) cc_final: 0.8241 (m100) REVERT: g 52 PHE cc_start: 0.8598 (m-80) cc_final: 0.8350 (m-80) REVERT: g 197 GLN cc_start: 0.9295 (mm-40) cc_final: 0.9052 (mm-40) REVERT: g 377 MET cc_start: 0.8432 (tmm) cc_final: 0.8045 (tmm) REVERT: g 392 CYS cc_start: 0.8508 (p) cc_final: 0.8233 (p) REVERT: g 397 LYS cc_start: 0.8723 (tttt) cc_final: 0.8318 (mmmt) REVERT: h 15 ASN cc_start: 0.8507 (m110) cc_final: 0.8071 (m110) REVERT: h 20 GLU cc_start: 0.8408 (tp30) cc_final: 0.8081 (tp30) REVERT: h 204 VAL cc_start: 0.9314 (t) cc_final: 0.9009 (t) REVERT: h 270 MET cc_start: 0.7676 (ttt) cc_final: 0.7470 (ttt) REVERT: h 271 THR cc_start: 0.7851 (p) cc_final: 0.7327 (p) outliers start: 4 outliers final: 0 residues processed: 321 average time/residue: 0.2222 time to fit residues: 108.6373 Evaluate side-chains 244 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 11 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13723 Z= 0.252 Angle : 0.617 6.569 18642 Z= 0.316 Chirality : 0.045 0.246 2079 Planarity : 0.004 0.051 2403 Dihedral : 10.092 166.394 1871 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.20 % Allowed : 4.64 % Favored : 95.16 % 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: -0.21 (0.21), residues: 1647 helix: 1.08 (0.18), residues: 764 sheet: -1.74 (0.32), residues: 248 loop : -0.87 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 21 HIS 0.009 0.001 HIS h 29 PHE 0.019 0.002 PHE g 225 TYR 0.017 0.001 TYR b 172 ARG 0.004 0.001 ARG g 244 *********************** 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 315 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 312 time to evaluate : 2.128 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 75 ILE cc_start: 0.8999 (mt) cc_final: 0.8798 (mt) REVERT: a 167 LEU cc_start: 0.9206 (mm) cc_final: 0.8898 (mm) REVERT: a 196 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6800 (mm-30) REVERT: a 203 MET cc_start: 0.8962 (mmp) cc_final: 0.7752 (mmp) REVERT: a 320 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8357 (mtp-110) REVERT: a 377 MET cc_start: 0.8775 (ttp) cc_final: 0.8511 (ttp) REVERT: b 152 LEU cc_start: 0.9712 (tp) cc_final: 0.9503 (tp) REVERT: b 185 TYR cc_start: 0.7717 (m-10) cc_final: 0.7289 (m-10) REVERT: b 203 MET cc_start: 0.9387 (mmp) cc_final: 0.8526 (mmm) REVERT: b 210 TYR cc_start: 0.8384 (m-80) cc_final: 0.7876 (m-80) REVERT: b 217 LEU cc_start: 0.8606 (mt) cc_final: 0.8288 (mt) REVERT: b 260 VAL cc_start: 0.8871 (t) cc_final: 0.8443 (p) REVERT: b 301 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8409 (pt0) REVERT: b 302 MET cc_start: 0.8789 (tpp) cc_final: 0.8443 (tpp) REVERT: b 351 PHE cc_start: 0.8467 (m-10) cc_final: 0.7655 (m-10) REVERT: g 197 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8731 (mm-40) REVERT: g 253 LEU cc_start: 0.8745 (tp) cc_final: 0.8223 (tp) REVERT: g 335 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9100 (mmmt) REVERT: g 392 CYS cc_start: 0.8458 (p) cc_final: 0.8159 (p) REVERT: g 397 LYS cc_start: 0.8667 (tttt) cc_final: 0.8249 (mmmt) REVERT: g 421 MET cc_start: 0.8995 (mtp) cc_final: 0.8664 (mtp) REVERT: h 15 ASN cc_start: 0.8496 (m110) cc_final: 0.8054 (m110) REVERT: h 20 GLU cc_start: 0.8478 (tp30) cc_final: 0.8093 (tp30) REVERT: h 141 ILE cc_start: 0.9475 (pt) cc_final: 0.9188 (pt) REVERT: h 178 MET cc_start: 0.5001 (ttp) cc_final: 0.4460 (ttm) REVERT: h 270 MET cc_start: 0.7666 (ttt) cc_final: 0.7382 (ttt) REVERT: h 271 THR cc_start: 0.7706 (p) cc_final: 0.7093 (p) outliers start: 3 outliers final: 0 residues processed: 313 average time/residue: 0.2346 time to fit residues: 110.7200 Evaluate side-chains 250 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 301 GLN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 ASN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2316 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= 0.230 Angle : 0.596 6.912 18642 Z= 0.305 Chirality : 0.045 0.250 2079 Planarity : 0.004 0.048 2403 Dihedral : 9.790 158.332 1871 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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: -0.11 (0.21), residues: 1647 helix: 1.12 (0.18), residues: 767 sheet: -1.40 (0.33), residues: 229 loop : -0.94 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 21 HIS 0.006 0.001 HIS g 371 PHE 0.019 0.001 PHE h 21 TYR 0.020 0.001 TYR g 169 ARG 0.004 0.000 ARG a 121 *********************** 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 314 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.428 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: a 69 ASP cc_start: 0.6770 (m-30) cc_final: 0.6406 (m-30) REVERT: a 167 LEU cc_start: 0.9188 (mm) cc_final: 0.8891 (mm) REVERT: a 196 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6827 (mm-30) REVERT: a 203 MET cc_start: 0.9001 (mmp) cc_final: 0.7893 (mmp) REVERT: a 293 ASN cc_start: 0.9156 (t0) cc_final: 0.8881 (t0) REVERT: a 415 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7602 (mt-10) REVERT: b 152 LEU cc_start: 0.9711 (tp) cc_final: 0.9500 (tp) REVERT: b 185 TYR cc_start: 0.7575 (m-10) cc_final: 0.7232 (m-10) REVERT: b 210 TYR cc_start: 0.8450 (m-80) cc_final: 0.8021 (m-80) REVERT: b 217 LEU cc_start: 0.8627 (mt) cc_final: 0.8318 (mt) REVERT: b 260 VAL cc_start: 0.8918 (t) cc_final: 0.8488 (p) REVERT: b 290 GLU cc_start: 0.8851 (pt0) cc_final: 0.8622 (pt0) REVERT: b 301 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8396 (pt0) REVERT: b 302 MET cc_start: 0.8787 (tpp) cc_final: 0.8413 (tpp) REVERT: b 351 PHE cc_start: 0.8443 (m-10) cc_final: 0.7674 (m-10) REVERT: g 15 ASN cc_start: 0.9056 (m110) cc_final: 0.8724 (m110) REVERT: g 22 TRP cc_start: 0.8536 (m100) cc_final: 0.8131 (m100) REVERT: g 103 ASN cc_start: 0.7497 (m110) cc_final: 0.7180 (m110) REVERT: g 197 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8748 (mm-40) REVERT: g 335 LYS cc_start: 0.9413 (mmpt) cc_final: 0.9186 (mmmt) REVERT: g 377 MET cc_start: 0.8370 (tmm) cc_final: 0.8088 (tmm) REVERT: g 392 CYS cc_start: 0.8377 (p) cc_final: 0.8142 (p) REVERT: g 397 LYS cc_start: 0.8566 (tttt) cc_final: 0.8219 (mmmt) REVERT: g 421 MET cc_start: 0.8977 (mtp) cc_final: 0.8743 (mtp) REVERT: h 15 ASN cc_start: 0.8356 (m110) cc_final: 0.7893 (m110) REVERT: h 20 GLU cc_start: 0.8364 (tp30) cc_final: 0.7977 (tp30) REVERT: h 270 MET cc_start: 0.7651 (ttt) cc_final: 0.7400 (ttt) REVERT: h 271 THR cc_start: 0.7746 (p) cc_final: 0.7263 (p) REVERT: h 292 ASP cc_start: 0.9144 (p0) cc_final: 0.8936 (p0) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2349 time to fit residues: 110.3370 Evaluate side-chains 252 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 11 GLN a 186 ASN a 233 GLN ** a 356 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13723 Z= 0.207 Angle : 0.602 7.003 18642 Z= 0.306 Chirality : 0.045 0.208 2079 Planarity : 0.004 0.046 2403 Dihedral : 9.572 156.967 1871 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: 1.15 (0.19), residues: 769 sheet: -1.29 (0.35), residues: 220 loop : -0.75 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 21 HIS 0.006 0.001 HIS h 115 PHE 0.017 0.001 PHE a 351 TYR 0.016 0.001 TYR g 169 ARG 0.008 0.000 ARG a 121 *********************** 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 318 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.371 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: 0.6812 (m-30) cc_final: 0.6303 (m-30) REVERT: a 167 LEU cc_start: 0.9053 (mm) cc_final: 0.8631 (mm) REVERT: a 196 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6920 (mm-30) REVERT: b 127 ASP cc_start: 0.9080 (p0) cc_final: 0.8823 (p0) REVERT: b 152 LEU cc_start: 0.9703 (tp) cc_final: 0.9423 (tp) REVERT: b 185 TYR cc_start: 0.7541 (m-10) cc_final: 0.7215 (m-10) REVERT: b 210 TYR cc_start: 0.8465 (m-80) cc_final: 0.7987 (m-80) REVERT: b 217 LEU cc_start: 0.8602 (mt) cc_final: 0.8286 (mt) REVERT: b 260 VAL cc_start: 0.8891 (t) cc_final: 0.8473 (p) REVERT: b 301 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8385 (pt0) REVERT: b 302 MET cc_start: 0.8724 (tpp) cc_final: 0.8428 (tpp) REVERT: b 422 ARG cc_start: 0.8637 (tpt90) cc_final: 0.8163 (tmm160) REVERT: g 22 TRP cc_start: 0.8477 (m100) cc_final: 0.7862 (m100) REVERT: g 103 ASN cc_start: 0.7493 (m110) cc_final: 0.7123 (m-40) REVERT: g 197 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8733 (mm-40) REVERT: g 335 LYS cc_start: 0.9392 (mmpt) cc_final: 0.9175 (mmmt) REVERT: g 392 CYS cc_start: 0.8378 (p) cc_final: 0.8121 (p) REVERT: g 397 LYS cc_start: 0.8529 (tttt) cc_final: 0.8190 (mmmt) REVERT: g 421 MET cc_start: 0.8933 (mtp) cc_final: 0.8688 (mtp) REVERT: h 15 ASN cc_start: 0.8622 (m110) cc_final: 0.8237 (m110) REVERT: h 20 GLU cc_start: 0.8223 (tp30) cc_final: 0.7714 (tp30) REVERT: h 270 MET cc_start: 0.7532 (ttt) cc_final: 0.7291 (ttt) REVERT: h 271 THR cc_start: 0.7555 (p) cc_final: 0.7340 (p) REVERT: h 279 ASP cc_start: 0.7454 (m-30) cc_final: 0.7078 (t0) REVERT: h 292 ASP cc_start: 0.9130 (p0) cc_final: 0.8836 (p0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2302 time to fit residues: 109.7478 Evaluate side-chains 259 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 61 HIS a 186 ASN a 233 GLN ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS ** g 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 167 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13723 Z= 0.210 Angle : 0.608 7.812 18642 Z= 0.310 Chirality : 0.044 0.191 2079 Planarity : 0.004 0.043 2403 Dihedral : 9.433 156.433 1871 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.07 % Allowed : 2.11 % Favored : 97.82 % 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: 0.03 (0.21), residues: 1647 helix: 1.13 (0.19), residues: 769 sheet: -1.22 (0.34), residues: 225 loop : -0.78 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 21 HIS 0.006 0.001 HIS g 115 PHE 0.021 0.001 PHE h 21 TYR 0.025 0.001 TYR g 169 ARG 0.005 0.000 ARG a 214 *********************** 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 318 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 1.619 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: 0.6765 (m-30) cc_final: 0.6205 (m-30) REVERT: a 254 ASP cc_start: 0.7294 (t70) cc_final: 0.6878 (t70) REVERT: a 280 LYS cc_start: 0.0759 (tptm) cc_final: 0.0513 (tptp) REVERT: a 377 MET cc_start: 0.8816 (ttp) cc_final: 0.8616 (ttp) REVERT: b 152 LEU cc_start: 0.9712 (tp) cc_final: 0.9440 (tp) REVERT: b 157 LEU cc_start: 0.9019 (mt) cc_final: 0.8769 (mt) REVERT: b 183 GLU cc_start: 0.8668 (mp0) cc_final: 0.8359 (mp0) REVERT: b 185 TYR cc_start: 0.7578 (m-10) cc_final: 0.7011 (m-10) REVERT: b 210 TYR cc_start: 0.8217 (m-80) cc_final: 0.7674 (m-80) REVERT: b 217 LEU cc_start: 0.8578 (mt) cc_final: 0.8266 (mt) REVERT: b 260 VAL cc_start: 0.8907 (t) cc_final: 0.8483 (p) REVERT: b 295 CYS cc_start: 0.9094 (m) cc_final: 0.8772 (m) REVERT: b 301 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8323 (pt0) REVERT: b 302 MET cc_start: 0.8618 (tpp) cc_final: 0.8361 (tpp) REVERT: b 351 PHE cc_start: 0.8448 (m-10) cc_final: 0.7656 (m-10) REVERT: b 422 ARG cc_start: 0.8590 (tpt90) cc_final: 0.8208 (tmm160) REVERT: g 22 TRP cc_start: 0.8475 (m100) cc_final: 0.7824 (m100) REVERT: g 197 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8748 (mm-40) REVERT: g 297 LEU cc_start: 0.8371 (mp) cc_final: 0.8001 (mp) REVERT: g 335 LYS cc_start: 0.9406 (mmpt) cc_final: 0.9200 (mmmt) REVERT: g 392 CYS cc_start: 0.8307 (p) cc_final: 0.8099 (p) REVERT: g 397 LYS cc_start: 0.8537 (tttt) cc_final: 0.8191 (mmmt) REVERT: g 421 MET cc_start: 0.8936 (mtp) cc_final: 0.8698 (mtp) REVERT: h 15 ASN cc_start: 0.8627 (m110) cc_final: 0.8238 (m110) REVERT: h 20 GLU cc_start: 0.8157 (tp30) cc_final: 0.7583 (tp30) REVERT: h 85 LEU cc_start: 0.9372 (tp) cc_final: 0.9161 (tp) REVERT: h 178 MET cc_start: 0.5142 (ttp) cc_final: 0.4045 (ttm) REVERT: h 270 MET cc_start: 0.7589 (ttt) cc_final: 0.7332 (ttt) REVERT: h 279 ASP cc_start: 0.7375 (m-30) cc_final: 0.7022 (t0) REVERT: h 292 ASP cc_start: 0.9145 (p0) cc_final: 0.8857 (p0) REVERT: h 324 ILE cc_start: 0.9034 (mm) cc_final: 0.8805 (mm) REVERT: h 377 MET cc_start: 0.8687 (ppp) cc_final: 0.8440 (ppp) outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.2310 time to fit residues: 110.3858 Evaluate side-chains 266 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 116 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 0.0030 chunk 98 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 g 103 ASN g 175 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13723 Z= 0.199 Angle : 0.614 8.204 18642 Z= 0.312 Chirality : 0.044 0.190 2079 Planarity : 0.004 0.042 2403 Dihedral : 9.275 155.506 1871 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: 0.10 (0.21), residues: 1647 helix: 1.14 (0.19), residues: 764 sheet: -0.99 (0.35), residues: 223 loop : -0.75 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 21 HIS 0.007 0.001 HIS g 115 PHE 0.019 0.001 PHE h 21 TYR 0.029 0.001 TYR g 169 ARG 0.008 0.000 ARG a 214 *********************** 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 333 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 1.550 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 21 TRP cc_start: 0.8503 (m100) cc_final: 0.7992 (m100) REVERT: a 69 ASP cc_start: 0.6735 (m-30) cc_final: 0.6117 (m-30) REVERT: a 186 ASN cc_start: 0.8684 (m-40) cc_final: 0.8479 (m110) REVERT: a 377 MET cc_start: 0.8650 (ttp) cc_final: 0.8342 (ttp) REVERT: a 415 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7417 (mt-10) REVERT: b 185 TYR cc_start: 0.7575 (m-10) cc_final: 0.7248 (m-10) REVERT: b 187 SER cc_start: 0.9140 (m) cc_final: 0.8858 (p) REVERT: b 210 TYR cc_start: 0.8255 (m-80) cc_final: 0.7674 (m-80) REVERT: b 217 LEU cc_start: 0.8552 (mt) cc_final: 0.8262 (mt) REVERT: b 254 ASP cc_start: 0.8585 (m-30) cc_final: 0.8382 (m-30) REVERT: b 260 VAL cc_start: 0.8936 (t) cc_final: 0.8520 (p) REVERT: b 301 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8312 (pt0) REVERT: b 302 MET cc_start: 0.8548 (tpp) cc_final: 0.8286 (tpp) REVERT: b 313 MET cc_start: 0.7772 (mpp) cc_final: 0.7496 (mpp) REVERT: g 22 TRP cc_start: 0.8413 (m100) cc_final: 0.7859 (m100) REVERT: g 197 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8730 (mm-40) REVERT: g 236 MET cc_start: 0.8823 (mmm) cc_final: 0.7182 (mmm) REVERT: g 297 LEU cc_start: 0.8420 (mp) cc_final: 0.8113 (mp) REVERT: g 335 LYS cc_start: 0.9400 (mmpt) cc_final: 0.9195 (mmmt) REVERT: g 397 LYS cc_start: 0.8550 (tttt) cc_final: 0.7892 (mmmt) REVERT: g 421 MET cc_start: 0.8916 (mtp) cc_final: 0.8660 (mtp) REVERT: h 20 GLU cc_start: 0.8172 (tp30) cc_final: 0.7586 (tp30) REVERT: h 85 LEU cc_start: 0.9370 (tp) cc_final: 0.9164 (tp) REVERT: h 167 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8258 (mm-40) REVERT: h 271 THR cc_start: 0.7604 (p) cc_final: 0.7383 (p) REVERT: h 279 ASP cc_start: 0.7291 (m-30) cc_final: 0.6942 (t0) REVERT: h 292 ASP cc_start: 0.9142 (p0) cc_final: 0.8846 (p0) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2276 time to fit residues: 113.6808 Evaluate side-chains 269 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 HIS ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13723 Z= 0.193 Angle : 0.625 8.471 18642 Z= 0.316 Chirality : 0.045 0.184 2079 Planarity : 0.004 0.042 2403 Dihedral : 9.130 154.658 1871 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 0.06 (0.21), residues: 1647 helix: 1.02 (0.18), residues: 768 sheet: -1.00 (0.34), residues: 241 loop : -0.64 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 346 HIS 0.005 0.001 HIS a 192 PHE 0.021 0.001 PHE h 21 TYR 0.023 0.001 TYR b 399 ARG 0.008 0.001 ARG a 214 *********************** 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 328 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.688 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: a 21 TRP cc_start: 0.8496 (m100) cc_final: 0.8072 (m100) REVERT: a 69 ASP cc_start: 0.6617 (m-30) cc_final: 0.6069 (m-30) REVERT: a 280 LYS cc_start: -0.0472 (tptm) cc_final: -0.1069 (tptp) REVERT: a 377 MET cc_start: 0.8834 (ttp) cc_final: 0.8564 (ttp) REVERT: a 415 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7368 (mt-10) REVERT: b 152 LEU cc_start: 0.9618 (tp) cc_final: 0.9332 (tp) REVERT: b 185 TYR cc_start: 0.7630 (m-10) cc_final: 0.7293 (m-10) REVERT: b 217 LEU cc_start: 0.8601 (mt) cc_final: 0.8290 (mt) REVERT: b 260 VAL cc_start: 0.8936 (t) cc_final: 0.8548 (p) REVERT: b 295 CYS cc_start: 0.9058 (m) cc_final: 0.8776 (m) REVERT: b 301 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8268 (pt0) REVERT: b 302 MET cc_start: 0.8647 (tpp) cc_final: 0.8426 (tpp) REVERT: b 313 MET cc_start: 0.7866 (mpp) cc_final: 0.7516 (mpp) REVERT: g 22 TRP cc_start: 0.8406 (m100) cc_final: 0.7845 (m100) REVERT: g 169 TYR cc_start: 0.7661 (m-10) cc_final: 0.7000 (m-10) REVERT: g 197 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8788 (mm-40) REVERT: g 206 ASP cc_start: 0.7820 (t0) cc_final: 0.7608 (t0) REVERT: g 236 MET cc_start: 0.8539 (mmm) cc_final: 0.6667 (mmm) REVERT: g 297 LEU cc_start: 0.8130 (mp) cc_final: 0.7911 (mp) REVERT: g 335 LYS cc_start: 0.9376 (mmpt) cc_final: 0.9175 (mmmt) REVERT: g 397 LYS cc_start: 0.8535 (tttt) cc_final: 0.7819 (mmmt) REVERT: g 421 MET cc_start: 0.8914 (mtp) cc_final: 0.8689 (mtp) REVERT: h 15 ASN cc_start: 0.8990 (m110) cc_final: 0.8536 (m110) REVERT: h 20 GLU cc_start: 0.8195 (tp30) cc_final: 0.7579 (tp30) REVERT: h 85 LEU cc_start: 0.9357 (tp) cc_final: 0.9149 (tp) REVERT: h 167 GLN cc_start: 0.8377 (mm110) cc_final: 0.8173 (mm110) REVERT: h 193 LYS cc_start: 0.9344 (tptp) cc_final: 0.8891 (tttm) REVERT: h 271 THR cc_start: 0.7822 (p) cc_final: 0.7396 (p) REVERT: h 279 ASP cc_start: 0.7317 (m-30) cc_final: 0.6994 (t0) REVERT: h 292 ASP cc_start: 0.9128 (p0) cc_final: 0.8844 (p0) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2310 time to fit residues: 114.6164 Evaluate side-chains 257 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** b 216 ASN g 15 ASN g 103 ASN ** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13723 Z= 0.230 Angle : 0.651 9.583 18642 Z= 0.334 Chirality : 0.045 0.250 2079 Planarity : 0.004 0.042 2403 Dihedral : 9.097 155.041 1871 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.03 (0.21), residues: 1647 helix: 0.96 (0.19), residues: 764 sheet: -1.00 (0.35), residues: 224 loop : -0.72 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 346 HIS 0.006 0.001 HIS g 115 PHE 0.017 0.002 PHE g 119 TYR 0.026 0.001 TYR g 169 ARG 0.007 0.001 ARG a 214 *********************** 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 314 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.609 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 21 TRP cc_start: 0.8505 (m100) cc_final: 0.8139 (m100) REVERT: a 69 ASP cc_start: 0.6681 (m-30) cc_final: 0.6092 (m-30) REVERT: a 186 ASN cc_start: 0.8658 (m-40) cc_final: 0.8447 (m110) REVERT: a 377 MET cc_start: 0.8777 (ttp) cc_final: 0.8523 (ttp) REVERT: a 415 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7391 (mt-10) REVERT: b 152 LEU cc_start: 0.9557 (tp) cc_final: 0.9278 (tp) REVERT: b 157 LEU cc_start: 0.9112 (mt) cc_final: 0.8900 (mt) REVERT: b 183 GLU cc_start: 0.8634 (mp0) cc_final: 0.8228 (mp0) REVERT: b 185 TYR cc_start: 0.7620 (m-10) cc_final: 0.7277 (m-10) REVERT: b 217 LEU cc_start: 0.8571 (mt) cc_final: 0.8274 (mt) REVERT: b 260 VAL cc_start: 0.9026 (t) cc_final: 0.8576 (p) REVERT: b 295 CYS cc_start: 0.9099 (m) cc_final: 0.8807 (m) REVERT: b 301 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8297 (pt0) REVERT: b 302 MET cc_start: 0.8614 (tpp) cc_final: 0.8396 (tpp) REVERT: b 313 MET cc_start: 0.7903 (mpp) cc_final: 0.7543 (mpp) REVERT: b 347 CYS cc_start: 0.8543 (t) cc_final: 0.8243 (t) REVERT: g 22 TRP cc_start: 0.8420 (m100) cc_final: 0.7905 (m100) REVERT: g 169 TYR cc_start: 0.7735 (m-10) cc_final: 0.6516 (m-80) REVERT: g 197 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8766 (mm-40) REVERT: g 236 MET cc_start: 0.8506 (mmm) cc_final: 0.7143 (mmm) REVERT: g 397 LYS cc_start: 0.8540 (tttt) cc_final: 0.7850 (mmmt) REVERT: g 421 MET cc_start: 0.8886 (mtp) cc_final: 0.8647 (mtp) REVERT: h 15 ASN cc_start: 0.8903 (m110) cc_final: 0.8569 (m110) REVERT: h 20 GLU cc_start: 0.8204 (tp30) cc_final: 0.7875 (tp30) REVERT: h 22 TRP cc_start: 0.8796 (m100) cc_final: 0.8541 (m100) REVERT: h 85 LEU cc_start: 0.9378 (tp) cc_final: 0.9153 (tp) REVERT: h 167 GLN cc_start: 0.8381 (mm110) cc_final: 0.8170 (mm-40) REVERT: h 271 THR cc_start: 0.8001 (p) cc_final: 0.7533 (p) REVERT: h 279 ASP cc_start: 0.7330 (m-30) cc_final: 0.6996 (t0) REVERT: h 292 ASP cc_start: 0.9133 (p0) cc_final: 0.8836 (p0) REVERT: h 322 ASN cc_start: 0.7474 (t0) cc_final: 0.7266 (t0) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2194 time to fit residues: 105.5855 Evaluate side-chains 262 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13723 Z= 0.242 Angle : 0.662 9.086 18642 Z= 0.338 Chirality : 0.046 0.348 2079 Planarity : 0.004 0.042 2403 Dihedral : 9.092 155.485 1871 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.10 (0.21), residues: 1647 helix: 0.91 (0.19), residues: 763 sheet: -1.30 (0.33), residues: 240 loop : -0.63 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 346 HIS 0.004 0.001 HIS a 283 PHE 0.019 0.002 PHE h 21 TYR 0.026 0.002 TYR b 399 ARG 0.007 0.001 ARG a 214 ********************** 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 311 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.621 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: 0.6274 (m-30) cc_final: 0.5702 (m-30) REVERT: a 377 MET cc_start: 0.8945 (ttp) cc_final: 0.8707 (ttp) REVERT: a 415 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7411 (mt-10) REVERT: b 157 LEU cc_start: 0.9116 (mt) cc_final: 0.8904 (mt) REVERT: b 183 GLU cc_start: 0.8611 (mp0) cc_final: 0.8198 (mp0) REVERT: b 185 TYR cc_start: 0.7665 (m-10) cc_final: 0.7320 (m-10) REVERT: b 217 LEU cc_start: 0.8578 (mt) cc_final: 0.8293 (mt) REVERT: b 260 VAL cc_start: 0.9032 (t) cc_final: 0.8581 (p) REVERT: b 301 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8289 (pt0) REVERT: b 302 MET cc_start: 0.8598 (tpp) cc_final: 0.8352 (tpp) REVERT: g 20 GLU cc_start: 0.8266 (pm20) cc_final: 0.7954 (pm20) REVERT: g 169 TYR cc_start: 0.7817 (m-10) cc_final: 0.6504 (m-10) REVERT: g 205 LEU cc_start: 0.9091 (mt) cc_final: 0.8869 (mt) REVERT: g 236 MET cc_start: 0.8502 (mmm) cc_final: 0.7175 (mmm) REVERT: g 397 LYS cc_start: 0.8451 (tttt) cc_final: 0.7756 (mmmt) REVERT: g 421 MET cc_start: 0.8908 (mtp) cc_final: 0.8671 (mtp) REVERT: h 20 GLU cc_start: 0.8179 (tp30) cc_final: 0.7883 (tp30) REVERT: h 22 TRP cc_start: 0.8815 (m100) cc_final: 0.8525 (m100) REVERT: h 85 LEU cc_start: 0.9414 (tp) cc_final: 0.9202 (tp) REVERT: h 167 GLN cc_start: 0.8406 (mm110) cc_final: 0.8185 (mm110) REVERT: h 271 THR cc_start: 0.7960 (p) cc_final: 0.7322 (p) REVERT: h 279 ASP cc_start: 0.7390 (m-30) cc_final: 0.6900 (t0) REVERT: h 292 ASP cc_start: 0.9111 (p0) cc_final: 0.8838 (p0) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2277 time to fit residues: 108.2454 Evaluate side-chains 250 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 16 optimal weight: 0.0040 chunk 24 optimal weight: 0.2980 chunk 115 optimal weight: 0.0980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 GLN ** h 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.079656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069871 restraints weight = 52248.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071888 restraints weight = 31781.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073342 restraints weight = 21500.325| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13723 Z= 0.192 Angle : 0.643 9.232 18642 Z= 0.326 Chirality : 0.046 0.285 2079 Planarity : 0.004 0.041 2403 Dihedral : 8.966 154.035 1871 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.03 (0.21), residues: 1647 helix: 0.99 (0.19), residues: 767 sheet: -1.23 (0.32), residues: 258 loop : -0.49 (0.25), residues: 622 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 0.027 0.001 PHE g 119 TYR 0.025 0.001 TYR b 399 ARG 0.007 0.000 ARG a 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2982.57 seconds wall clock time: 56 minutes 2.45 seconds (3362.45 seconds total)