Starting phenix.real_space_refine on Wed Jul 1 23:50:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eyj_50055/07_2026/9eyj_50055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eyj_50055/07_2026/9eyj_50055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eyj_50055/07_2026/9eyj_50055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eyj_50055/07_2026/9eyj_50055.map" model { file = "/net/cci-nas-00/data/ceres_data/9eyj_50055/07_2026/9eyj_50055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eyj_50055/07_2026/9eyj_50055.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 14 5.16 5 C 2811 2.51 5 N 743 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4334 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2301 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 15, 'ASP:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1945 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 6 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 18, 'GLN:plan1': 14, 'ASP:plan': 4, 'ASN:plan1': 5, 'PHE:plan': 3, 'TYR:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 226 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Time building chain proxies: 1.08, per 1000 atoms: 0.25 Number of scatterers: 4334 At special positions: 0 Unit cell: (59.4, 78.1, 85.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 4 15.00 O 762 8.00 N 743 7.00 C 2811 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: 0.32 Conformation dependent library (CDL) restraints added in 98.3 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 45.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.676A pdb=" N LYS A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.499A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.028A pdb=" N LEU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.637A pdb=" N ASN A 362 " --> pdb=" O GLN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 433 through 448 Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.834A pdb=" N LEU B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 250 removed outlier: 3.939A pdb=" N LYS B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.687A pdb=" N ALA B 270 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 4.067A pdb=" N GLN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.455A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.535A pdb=" N LEU B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 433 through 451 removed outlier: 3.705A pdb=" N LEU B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 475 Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 222 removed outlier: 7.751A pdb=" N SER A 334 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TRP A 310 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 336 " --> pdb=" O TRP A 310 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR A 312 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N MET A 338 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 333 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 350 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 335 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 230 removed outlier: 7.054A pdb=" N ILE A 226 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLY A 273 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 228 " --> pdb=" O GLY A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 373 through 378 removed outlier: 4.005A pdb=" N ALA A 420 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN A 460 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 498 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 220 through 227 removed outlier: 3.836A pdb=" N LEU B 309 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 223 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 311 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER B 334 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP B 310 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 336 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 312 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL B 333 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE B 350 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 335 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 373 through 378 removed outlier: 6.974A pdb=" N GLU B 386 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU B 416 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY B 388 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE B 418 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 390 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ALA B 420 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N TYR B 392 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 456 " --> pdb=" O ASP B 481 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 498 " --> pdb=" O VAL B 482 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 564 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: 0.62 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 728 1.32 - 1.44: 1250 1.44 - 1.57: 2441 1.57 - 1.69: 7 1.69 - 1.81: 22 Bond restraints: 4448 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" N LYS B 330 " ideal model delta sigma weight residual 1.334 1.237 0.096 1.30e-02 5.92e+03 5.50e+01 bond pdb=" CA LYS B 330 " pdb=" CB LYS B 330 " ideal model delta sigma weight residual 1.529 1.469 0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N LYS B 330 " pdb=" CA LYS B 330 " ideal model delta sigma weight residual 1.457 1.408 0.049 1.16e-02 7.43e+03 1.78e+01 bond pdb=" CA GLN A 409 " pdb=" CB GLN A 409 " ideal model delta sigma weight residual 1.536 1.494 0.042 1.46e-02 4.69e+03 8.35e+00 bond pdb=" C GLN A 409 " pdb=" O GLN A 409 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.23e-02 6.61e+03 7.41e+00 ... (remaining 4443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 5990 1.81 - 3.63: 89 3.63 - 5.44: 11 5.44 - 7.25: 4 7.25 - 9.07: 1 Bond angle restraints: 6095 Sorted by residual: angle pdb=" N LYS B 330 " pdb=" CA LYS B 330 " pdb=" CB LYS B 330 " ideal model delta sigma weight residual 110.92 101.85 9.07 1.60e+00 3.91e-01 3.21e+01 angle pdb=" CA PRO A 479 " pdb=" C PRO A 479 " pdb=" O PRO A 479 " ideal model delta sigma weight residual 123.07 120.12 2.95 1.38e+00 5.25e-01 4.58e+00 angle pdb=" C ALA B 281 " pdb=" N ASN B 282 " pdb=" CA ASN B 282 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.53e+00 angle pdb=" N9 A D 3 " pdb=" C4 A D 3 " pdb=" N3 A D 3 " ideal model delta sigma weight residual 127.40 129.09 -1.69 8.00e-01 1.56e+00 4.49e+00 angle pdb=" C TRP B 284 " pdb=" N GLN B 285 " pdb=" CA GLN B 285 " ideal model delta sigma weight residual 120.31 117.10 3.21 1.52e+00 4.33e-01 4.46e+00 ... (remaining 6090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 2228 16.56 - 33.11: 223 33.11 - 49.67: 73 49.67 - 66.22: 21 66.22 - 82.78: 5 Dihedral angle restraints: 2550 sinusoidal: 859 harmonic: 1691 Sorted by residual: dihedral pdb=" N LYS B 330 " pdb=" C LYS B 330 " pdb=" CA LYS B 330 " pdb=" CB LYS B 330 " ideal model delta harmonic sigma weight residual 122.80 111.67 11.13 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" CA GLU B 280 " pdb=" C GLU B 280 " pdb=" N ALA B 281 " pdb=" CA ALA B 281 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLN A 460 " pdb=" C GLN A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 436 0.034 - 0.068: 191 0.068 - 0.103: 49 0.103 - 0.137: 26 0.137 - 0.171: 2 Chirality restraints: 704 Sorted by residual: chirality pdb=" CA GLN A 409 " pdb=" N GLN A 409 " pdb=" C GLN A 409 " pdb=" CB GLN A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CG LEU B 360 " pdb=" CB LEU B 360 " pdb=" CD1 LEU B 360 " pdb=" CD2 LEU B 360 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA ILE A 456 " pdb=" N ILE A 456 " pdb=" C ILE A 456 " pdb=" CB ILE A 456 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 701 not shown) Planarity restraints: 759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 363 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C VAL A 363 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 363 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 364 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 304 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.57e+00 pdb=" N PRO B 305 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 281 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C ALA B 281 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA B 281 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN B 282 " 0.008 2.00e-02 2.50e+03 ... (remaining 756 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 4 2.24 - 2.90: 1717 2.90 - 3.57: 6194 3.57 - 4.23: 10496 4.23 - 4.90: 17794 Nonbonded interactions: 36205 Sorted by model distance: nonbonded pdb=" P A D 1 " pdb=" O3' A D 4 " model vdw 1.569 3.400 nonbonded pdb=" O PHE A 477 " pdb=" CD1 LEU A 478 " model vdw 1.812 3.460 nonbonded pdb=" O ASP B 268 " pdb=" OD1 ASP B 268 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR A 392 " pdb=" OD1 ASN B 445 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A 345 " pdb=" N7 A D 3 " model vdw 2.298 3.120 ... (remaining 36200 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' and (resid 202 through 207 or (resid 208 through 211 and (name N or n \ ame CA or name C or name O or name CB )) or resid 212 or (resid 213 through 214 \ and (name N or name CA or name C or name O or name CB )) or resid 215 or (resid \ 216 and (name N or name CA or name C or name O or name CB )) or resid 217 throug \ h 229 or (resid 233 through 234 and (name N or name CA or name C or name O or na \ me CB )) or resid 235 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 through 241 or (resid 242 through 244 and \ (name N or name CA or name C or name O or name CB )) or resid 245 through 246 or \ (resid 247 through 249 and (name N or name CA or name C or name O or name CB )) \ or resid 250 through 256 or (resid 257 and (name N or name CA or name C or name \ O or name CB )) or resid 258 or (resid 259 through 260 and (name N or name CA o \ r name C or name O or name CB )) or resid 261 through 263 or (resid 264 through \ 265 and (name N or name CA or name C or name O or name CB )) or resid 266 throug \ h 270 or (resid 271 through 272 and (name N or name CA or name C or name O or na \ me CB )) or resid 273 or (resid 279 through 283 and (name N or name CA or name C \ or name O or name CB )) or resid 284 through 285 or (resid 286 and (name N or n \ ame CA or name C or name O or name CB )) or resid 287 through 290 or (resid 291 \ and (name N or name CA or name C or name O or name CB )) or resid 292 through 29 \ 9 or (resid 300 through 302 and (name N or name CA or name C or name O or name C \ B )) or resid 303 through 305 or (resid 306 through 308 and (name N or name CA o \ r name C or name O or name CB )) or resid 309 through 314 or (resid 315 through \ 316 and (name N or name CA or name C or name O or name CB )) or resid 317 or (re \ sid 318 through 320 and (name N or name CA or name C or name O or name CB )) or \ resid 321 through 322 or (resid 323 and (name N or name CA or name C or name O o \ r name CB )) or (resid 324 through 326 and (name N or name CA or name C or name \ O or name CB )) or resid 327 through 335 or (resid 336 through 337 and (name N o \ r name CA or name C or name O or name CB )) or (resid 344 through 345 and (name \ N or name CA or name C or name O or name CB )) or resid 346 through 371 or (resi \ d 372 and (name N or name CA or name C or name O or name CB )) or resid 373 thro \ ugh 375 or (resid 376 and (name N or name CA or name C or name O or name CB )) o \ r resid 377 or (resid 378 and (name N or name CA or name C or name O or name CB \ )) or resid 379 through 380 or (resid 381 and (name N or name CA or name C or na \ me O or name CB )) or resid 382 or (resid 383 through 384 and (name N or name CA \ or name C or name O or name CB )) or resid 385 or (resid 386 and (name N or nam \ e CA or name C or name O or name CB )) or resid 387 through 391 or (resid 392 an \ d (name N or name CA or name C or name O or name CB )) or resid 393 through 395 \ or (resid 396 and (name N or name CA or name C or name O or name CB )) or resid \ 397 through 398 or (resid 399 and (name N or name CA or name C or name O or name \ CB )) or resid 400 or (resid 401 through 405 and (name N or name CA or name C o \ r name O or name CB )) or resid 406 or (resid 407 through 412 and (name N or nam \ e CA or name C or name O or name CB )) or resid 413 or (resid 414 through 415 an \ d (name N or name CA or name C or name O or name CB )) or resid 416 through 418 \ or (resid 419 through 422 and (name N or name CA or name C or name O or name CB \ )) or (resid 426 and (name N or name CA or name C or name O or name CB )) or res \ id 427 through 485 or (resid 486 and (name N or name CA or name C or name O or n \ ame CB )) or resid 496 through 504)) selection = (chain 'B' and ((resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 233 or (resid 234 and (name N or name CA or name C or n \ ame O or name CB )) or resid 235 through 288 or (resid 289 through 291 and (name \ N or name CA or name C or name O or name CB )) or resid 292 through 301 or (res \ id 302 and (name N or name CA or name C or name O or name CB )) or resid 303 thr \ ough 307 or (resid 308 and (name N or name CA or name C or name O or name CB )) \ or resid 309 through 328 or (resid 329 and (name N or name CA or name C or name \ O or name CB )) or resid 330 through 351 or (resid 352 and (name N or name CA or \ name C or name O or name CB )) or (resid 357 through 358 and (name N or name CA \ or name C or name O or name CB )) or resid 359 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 or (resid 363 an \ d (name N or name CA or name C or name O or name CB )) or resid 364 through 365 \ or (resid 366 through 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 448 or (resid 449 through 450 and (name N or name CA or \ name C or name O or name CB )) or resid 451 through 504)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 : 0.004 0.096 4448 Z= 0.215 Angle : 0.587 9.068 6095 Z= 0.326 Chirality : 0.044 0.171 704 Planarity : 0.004 0.047 759 Dihedral : 16.128 82.780 1450 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.14 % Allowed : 24.87 % Favored : 72.99 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.35), residues: 558 helix: 0.55 (0.36), residues: 210 sheet: -0.76 (0.48), residues: 123 loop : -1.16 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 237 TYR 0.011 0.001 TYR A 436 PHE 0.009 0.001 PHE A 487 TRP 0.010 0.001 TRP B 284 HIS 0.003 0.001 HIS B 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.22 ( 4448) covalent geometry : angle 0.58694 / 0.33 ( 6095) hydrogen bonds : bond 0.16705 / 12.18 ( 199) hydrogen bonds : angle 7.70684 / 5.77 ( 564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.161 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 60 average time/residue: 0.2461 time to fit residues: 15.9320 Evaluate side-chains 44 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** B 239 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 = 0.4198 r_free = 0.4198 target = 0.137783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.126305 restraints weight = 9826.114| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.57 r_work: 0.3936 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4448 Z= 0.163 Angle : 0.549 5.265 6095 Z= 0.291 Chirality : 0.044 0.147 704 Planarity : 0.004 0.031 759 Dihedral : 8.351 71.569 650 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.88 % Allowed : 24.06 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.36), residues: 558 helix: 0.85 (0.36), residues: 213 sheet: -0.87 (0.49), residues: 119 loop : -1.15 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 331 TYR 0.014 0.001 TYR A 436 PHE 0.009 0.001 PHE B 389 TRP 0.010 0.001 TRP A 215 HIS 0.005 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 4448) covalent geometry : angle 0.54860 / 0.29 ( 6095) hydrogen bonds : bond 0.04393 / 3.20 ( 199) hydrogen bonds : angle 6.20552 / 4.61 ( 564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.167 Fit side-chains REVERT: A 242 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7584 (ttm) REVERT: A 323 ILE cc_start: 0.8391 (mm) cc_final: 0.7986 (mm) REVERT: B 351 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8631 (mt) outliers start: 22 outliers final: 12 residues processed: 56 average time/residue: 0.1577 time to fit residues: 9.8458 Evaluate side-chains 50 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 482 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.136938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.125687 restraints weight = 9691.655| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.51 r_work: 0.3931 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4448 Z= 0.165 Angle : 0.523 5.665 6095 Z= 0.278 Chirality : 0.043 0.136 704 Planarity : 0.004 0.031 759 Dihedral : 8.227 71.354 648 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 7.49 % Allowed : 22.99 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.36), residues: 558 helix: 0.90 (0.36), residues: 214 sheet: -1.21 (0.48), residues: 126 loop : -1.19 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 331 TYR 0.015 0.001 TYR A 436 PHE 0.010 0.001 PHE B 498 TRP 0.011 0.001 TRP A 215 HIS 0.003 0.001 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 4448) covalent geometry : angle 0.52305 / 0.28 ( 6095) hydrogen bonds : bond 0.04034 / 2.94 ( 199) hydrogen bonds : angle 5.88823 / 4.38 ( 564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 35 time to evaluate : 0.210 Fit side-chains REVERT: A 242 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7560 (ttm) REVERT: B 351 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8601 (mt) outliers start: 28 outliers final: 14 residues processed: 58 average time/residue: 0.1614 time to fit residues: 10.5079 Evaluate side-chains 50 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 482 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.137485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.126463 restraints weight = 9678.783| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.49 r_work: 0.3936 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4448 Z= 0.151 Angle : 0.509 5.241 6095 Z= 0.271 Chirality : 0.043 0.132 704 Planarity : 0.003 0.032 759 Dihedral : 8.228 71.794 648 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.68 % Allowed : 25.13 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.36), residues: 558 helix: 1.03 (0.37), residues: 214 sheet: -1.22 (0.47), residues: 125 loop : -1.21 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 455 TYR 0.015 0.001 TYR A 436 PHE 0.009 0.001 PHE A 261 TRP 0.009 0.001 TRP B 284 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 4448) covalent geometry : angle 0.50910 / 0.27 ( 6095) hydrogen bonds : bond 0.03769 / 2.76 ( 199) hydrogen bonds : angle 5.75818 / 4.28 ( 564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.155 Fit side-chains REVERT: A 242 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7533 (ttm) REVERT: B 351 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8565 (mt) outliers start: 25 outliers final: 16 residues processed: 55 average time/residue: 0.1786 time to fit residues: 11.0062 Evaluate side-chains 52 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 482 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 HIS ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.134162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123305 restraints weight = 9741.703| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.46 r_work: 0.3893 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4448 Z= 0.235 Angle : 0.597 6.764 6095 Z= 0.313 Chirality : 0.045 0.151 704 Planarity : 0.004 0.032 759 Dihedral : 8.476 71.993 648 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 8.29 % Allowed : 23.53 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.36), residues: 558 helix: 0.70 (0.36), residues: 214 sheet: -1.38 (0.47), residues: 124 loop : -1.37 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 495 TYR 0.018 0.002 TYR A 436 PHE 0.013 0.002 PHE A 261 TRP 0.017 0.002 TRP A 215 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 ( 4448) covalent geometry : angle 0.59740 / 0.31 ( 6095) hydrogen bonds : bond 0.04195 / 3.06 ( 199) hydrogen bonds : angle 6.03863 / 4.51 ( 564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 0.168 Fit side-chains REVERT: A 242 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7565 (ttm) REVERT: B 351 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8591 (mt) outliers start: 31 outliers final: 16 residues processed: 60 average time/residue: 0.1986 time to fit residues: 13.1834 Evaluate side-chains 52 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 484 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 31 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.0060 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.139115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.128081 restraints weight = 9807.851| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.52 r_work: 0.3959 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4448 Z= 0.105 Angle : 0.501 5.617 6095 Z= 0.268 Chirality : 0.043 0.131 704 Planarity : 0.003 0.033 759 Dihedral : 8.211 73.559 647 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.35 % Allowed : 26.20 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.36), residues: 558 helix: 1.14 (0.37), residues: 214 sheet: -1.31 (0.46), residues: 125 loop : -1.23 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 331 TYR 0.016 0.001 TYR B 451 PHE 0.009 0.001 PHE A 487 TRP 0.007 0.001 TRP B 284 HIS 0.004 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 4448) covalent geometry : angle 0.50062 / 0.27 ( 6095) hydrogen bonds : bond 0.03578 / 2.64 ( 199) hydrogen bonds : angle 5.54486 / 4.11 ( 564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.168 Fit side-chains REVERT: B 351 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8474 (mt) outliers start: 20 outliers final: 10 residues processed: 59 average time/residue: 0.2366 time to fit residues: 15.2045 Evaluate side-chains 45 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 GLN ** B 239 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 = 0.4201 r_free = 0.4201 target = 0.137811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.126853 restraints weight = 9870.838| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.52 r_work: 0.3949 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4448 Z= 0.132 Angle : 0.518 7.134 6095 Z= 0.271 Chirality : 0.043 0.163 704 Planarity : 0.003 0.033 759 Dihedral : 8.156 71.525 647 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.81 % Allowed : 27.54 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.36), residues: 558 helix: 1.14 (0.37), residues: 214 sheet: -1.20 (0.47), residues: 125 loop : -1.20 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.013 0.001 TYR A 436 PHE 0.008 0.001 PHE A 261 TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4448) covalent geometry : angle 0.51818 / 0.27 ( 6095) hydrogen bonds : bond 0.03623 / 2.67 ( 199) hydrogen bonds : angle 5.55346 / 4.12 ( 564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.166 Fit side-chains REVERT: A 476 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6623 (p90) REVERT: B 351 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8497 (mt) outliers start: 18 outliers final: 13 residues processed: 52 average time/residue: 0.1602 time to fit residues: 9.4561 Evaluate side-chains 50 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 484 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.138343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.127452 restraints weight = 9684.116| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.52 r_work: 0.3956 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4448 Z= 0.120 Angle : 0.514 7.049 6095 Z= 0.267 Chirality : 0.043 0.148 704 Planarity : 0.003 0.033 759 Dihedral : 8.124 71.729 647 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.28 % Allowed : 27.27 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.36), residues: 558 helix: 1.18 (0.36), residues: 215 sheet: -1.22 (0.47), residues: 125 loop : -1.11 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 237 TYR 0.013 0.001 TYR A 436 PHE 0.022 0.001 PHE A 340 TRP 0.009 0.001 TRP B 284 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 4448) covalent geometry : angle 0.51415 / 0.27 ( 6095) hydrogen bonds : bond 0.03556 / 2.64 ( 199) hydrogen bonds : angle 5.47598 / 4.06 ( 564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.159 Fit side-chains REVERT: B 351 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8491 (mt) outliers start: 16 outliers final: 9 residues processed: 51 average time/residue: 0.1521 time to fit residues: 8.6597 Evaluate side-chains 45 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 484 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.135542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124753 restraints weight = 9825.049| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.48 r_work: 0.3918 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4448 Z= 0.197 Angle : 0.580 6.960 6095 Z= 0.300 Chirality : 0.045 0.153 704 Planarity : 0.003 0.032 759 Dihedral : 8.295 71.300 647 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.55 % Allowed : 27.27 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.36), residues: 558 helix: 0.97 (0.36), residues: 216 sheet: -1.11 (0.48), residues: 119 loop : -1.18 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.016 0.002 TYR A 436 PHE 0.012 0.002 PHE A 340 TRP 0.017 0.002 TRP A 215 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 4448) covalent geometry : angle 0.58025 / 0.30 ( 6095) hydrogen bonds : bond 0.03912 / 2.88 ( 199) hydrogen bonds : angle 5.72789 / 4.27 ( 564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.172 Fit side-chains REVERT: B 351 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8525 (mt) outliers start: 17 outliers final: 12 residues processed: 50 average time/residue: 0.1909 time to fit residues: 10.6436 Evaluate side-chains 47 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 484 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.137841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.126980 restraints weight = 9752.749| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.50 r_work: 0.3946 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4448 Z= 0.124 Angle : 0.530 6.808 6095 Z= 0.277 Chirality : 0.043 0.144 704 Planarity : 0.003 0.032 759 Dihedral : 8.211 72.839 647 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.21 % Allowed : 28.34 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.36), residues: 558 helix: 1.19 (0.37), residues: 215 sheet: -1.16 (0.48), residues: 121 loop : -1.10 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 237 TYR 0.014 0.001 TYR A 436 PHE 0.010 0.001 PHE A 340 TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 4448) covalent geometry : angle 0.53010 / 0.28 ( 6095) hydrogen bonds : bond 0.03641 / 2.64 ( 199) hydrogen bonds : angle 5.50584 / 4.08 ( 564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.099 Fit side-chains REVERT: B 351 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8483 (mt) outliers start: 12 outliers final: 12 residues processed: 50 average time/residue: 0.1269 time to fit residues: 7.1864 Evaluate side-chains 48 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 31 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.137797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.126899 restraints weight = 9872.471| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.51 r_work: 0.3948 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4448 Z= 0.135 Angle : 0.526 6.799 6095 Z= 0.276 Chirality : 0.043 0.141 704 Planarity : 0.003 0.032 759 Dihedral : 8.171 71.719 647 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.48 % Allowed : 28.07 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.36), residues: 558 helix: 1.17 (0.37), residues: 215 sheet: -1.14 (0.48), residues: 121 loop : -1.13 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 237 TYR 0.017 0.001 TYR B 312 PHE 0.009 0.001 PHE A 340 TRP 0.009 0.001 TRP A 215 HIS 0.002 0.000 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 4448) covalent geometry : angle 0.52582 / 0.28 ( 6095) hydrogen bonds : bond 0.03665 / 2.67 ( 199) hydrogen bonds : angle 5.46880 / 4.06 ( 564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1102.33 seconds wall clock time: 19 minutes 36.16 seconds (1176.16 seconds total)