Starting phenix.real_space_refine on Mon Jan 13 22:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eyj_50055/01_2025/9eyj_50055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eyj_50055/01_2025/9eyj_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_50055/01_2025/9eyj_50055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eyj_50055/01_2025/9eyj_50055.map" model { file = "/net/cci-nas-00/data/ceres_data/9eyj_50055/01_2025/9eyj_50055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eyj_50055/01_2025/9eyj_50055.cif" } resolution = 2.97 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= 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} 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: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 3} 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: 3.22, per 1000 atoms: 0.74 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: 1.06 Conformation dependent library (CDL) restraints added in 577.1 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: 0.53 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: 1.21 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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=" 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 angle pdb=" C HIS B 457 " pdb=" N LEU B 458 " pdb=" CA LEU B 458 " ideal model delta sigma weight residual 122.07 118.52 3.55 1.71e+00 3.42e-01 4.30e+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: 0.640 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.640 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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= 0.269 Angle : 0.587 9.068 6095 Z= 0.319 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 (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: -0.70 (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 TRP 0.010 0.001 TRP B 284 HIS 0.003 0.001 HIS B 457 PHE 0.009 0.001 PHE A 487 TYR 0.011 0.001 TYR A 436 ARG 0.003 0.001 ARG A 237 *********************** 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 : 0.471 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 60 average time/residue: 0.6056 time to fit residues: 39.1538 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 : 0.483 ------------------------------------------------------------------------------- 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 47 optimal weight: 8.9990 chunk 42 optimal weight: 0.0370 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.140183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.129229 restraints weight = 9569.577| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.52 r_work: 0.3968 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4448 Z= 0.182 Angle : 0.494 5.161 6095 Z= 0.259 Chirality : 0.042 0.145 704 Planarity : 0.003 0.029 759 Dihedral : 8.130 70.664 650 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.61 % Allowed : 23.80 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.36), residues: 558 helix: 1.10 (0.36), residues: 214 sheet: -0.85 (0.47), residues: 128 loop : -1.09 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.003 0.001 HIS B 457 PHE 0.008 0.001 PHE A 261 TYR 0.012 0.001 TYR A 436 ARG 0.005 0.001 ARG B 331 *********************** 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 69 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7406 (ttm) REVERT: A 323 ILE cc_start: 0.8373 (mm) cc_final: 0.8005 (mm) REVERT: A 476 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6489 (p90) REVERT: B 351 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8600 (mt) outliers start: 21 outliers final: 13 residues processed: 60 average time/residue: 0.4606 time to fit residues: 30.5826 Evaluate side-chains 56 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 285 GLN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4174 r_free = 0.4174 target = 0.136092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.125015 restraints weight = 9636.636| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.48 r_work: 0.3919 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1635 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= 0.291 Angle : 0.552 6.210 6095 Z= 0.290 Chirality : 0.044 0.144 704 Planarity : 0.004 0.032 759 Dihedral : 8.336 73.040 648 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 7.22 % Allowed : 23.80 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.65 (0.36), residues: 558 helix: 0.89 (0.36), residues: 213 sheet: -1.21 (0.47), residues: 127 loop : -1.16 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.003 0.001 HIS A 396 PHE 0.010 0.001 PHE A 261 TYR 0.018 0.002 TYR A 436 ARG 0.003 0.001 ARG B 331 *********************** 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 64 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 37 time to evaluate : 0.470 Fit side-chains REVERT: A 242 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7562 (ttm) REVERT: A 348 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8208 (m) REVERT: A 476 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.6637 (p90) REVERT: B 285 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: B 351 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8550 (mt) outliers start: 27 outliers final: 13 residues processed: 58 average time/residue: 0.4504 time to fit residues: 28.9935 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 : 0.502 ------------------------------------------------------------------------------- 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 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 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 285 GLN 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 24 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 0.0570 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4207 r_free = 0.4207 target = 0.137944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.126411 restraints weight = 9684.071| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.54 r_work: 0.3950 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4448 Z= 0.201 Angle : 0.491 5.238 6095 Z= 0.257 Chirality : 0.042 0.131 704 Planarity : 0.003 0.030 759 Dihedral : 8.105 72.052 648 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 7.22 % Allowed : 24.33 % 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 (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: -0.41 (0.37), residues: 558 helix: 1.15 (0.37), residues: 214 sheet: -1.05 (0.47), residues: 125 loop : -1.14 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.002 0.001 HIS A 457 PHE 0.010 0.001 PHE A 261 TYR 0.014 0.001 TYR A 436 ARG 0.002 0.001 ARG B 331 *********************** 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 77 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.569 Fit side-chains REVERT: A 242 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7475 (ttm) REVERT: A 476 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6584 (p90) REVERT: B 351 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8489 (mt) outliers start: 27 outliers final: 11 residues processed: 69 average time/residue: 0.5717 time to fit residues: 42.6726 Evaluate side-chains 49 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 442 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 484 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4186 r_free = 0.4186 target = 0.136737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.125728 restraints weight = 9873.305| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.52 r_work: 0.3933 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1853 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= 0.241 Angle : 0.527 5.248 6095 Z= 0.276 Chirality : 0.043 0.134 704 Planarity : 0.003 0.032 759 Dihedral : 8.185 72.360 647 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.15 % Allowed : 26.47 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.53 (0.36), residues: 558 helix: 1.04 (0.37), residues: 215 sheet: -1.15 (0.47), residues: 128 loop : -1.17 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS A 457 PHE 0.020 0.002 PHE A 340 TYR 0.015 0.001 TYR A 436 ARG 0.002 0.000 ARG A 455 *********************** 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 62 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.479 Fit side-chains REVERT: A 242 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7485 (ttm) REVERT: A 259 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: B 351 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8488 (mt) REVERT: B 468 MET cc_start: 0.8186 (tmt) cc_final: 0.7982 (tpt) outliers start: 23 outliers final: 12 residues processed: 59 average time/residue: 0.4559 time to fit residues: 29.8018 Evaluate side-chains 52 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 259 GLU 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 226 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 442 SER 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 55 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 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 = 0.4186 r_free = 0.4186 target = 0.136642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.125654 restraints weight = 9735.463| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.53 r_work: 0.3933 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1956 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= 0.248 Angle : 0.542 7.644 6095 Z= 0.279 Chirality : 0.043 0.132 704 Planarity : 0.003 0.031 759 Dihedral : 8.227 72.486 647 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.68 % Allowed : 25.67 % 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 (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: -0.52 (0.37), residues: 558 helix: 1.08 (0.36), residues: 216 sheet: -1.22 (0.47), residues: 129 loop : -1.15 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.003 0.001 HIS A 346 PHE 0.009 0.001 PHE A 261 TYR 0.016 0.002 TYR B 312 ARG 0.001 0.000 ARG A 455 *********************** 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 64 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 0.479 Fit side-chains REVERT: A 242 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7483 (ttm) REVERT: B 351 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8498 (mt) outliers start: 25 outliers final: 13 residues processed: 60 average time/residue: 0.4212 time to fit residues: 28.2242 Evaluate side-chains 51 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET 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 226 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 482 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 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4204 r_free = 0.4204 target = 0.137888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.126588 restraints weight = 9643.750| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.54 r_work: 0.3954 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2013 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= 0.192 Angle : 0.514 6.695 6095 Z= 0.266 Chirality : 0.042 0.127 704 Planarity : 0.003 0.032 759 Dihedral : 8.083 72.182 647 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.81 % Allowed : 26.74 % 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 (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: -0.33 (0.36), residues: 558 helix: 1.24 (0.37), residues: 216 sheet: -0.98 (0.48), residues: 124 loop : -1.18 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.002 0.000 HIS B 457 PHE 0.013 0.001 PHE A 340 TYR 0.012 0.001 TYR A 436 ARG 0.002 0.000 ARG B 331 *********************** 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 59 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.476 Fit side-chains REVERT: A 503 MET cc_start: 0.8202 (mmt) cc_final: 0.7940 (mmp) REVERT: B 351 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8491 (mt) outliers start: 18 outliers final: 11 residues processed: 54 average time/residue: 0.5174 time to fit residues: 30.7109 Evaluate side-chains 45 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 442 SER 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 24 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.0050 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.139237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.128347 restraints weight = 9592.001| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.53 r_work: 0.3971 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2063 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= 0.185 Angle : 0.510 6.373 6095 Z= 0.263 Chirality : 0.042 0.126 704 Planarity : 0.003 0.032 759 Dihedral : 7.966 71.623 647 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.01 % Allowed : 28.07 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.26 (0.36), residues: 558 helix: 1.30 (0.37), residues: 216 sheet: -0.98 (0.47), residues: 126 loop : -1.10 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.002 0.000 HIS B 457 PHE 0.009 0.001 PHE A 340 TYR 0.011 0.001 TYR A 436 ARG 0.005 0.001 ARG A 237 *********************** 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 54 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.481 Fit side-chains REVERT: A 503 MET cc_start: 0.8208 (mmt) cc_final: 0.7965 (mmp) REVERT: B 268 ASP cc_start: 0.6846 (t70) cc_final: 0.6582 (t0) REVERT: B 351 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8461 (mt) outliers start: 15 outliers final: 10 residues processed: 53 average time/residue: 0.4633 time to fit residues: 27.2198 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 : 0.483 ------------------------------------------------------------------------------- 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 226 ILE 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 26 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.139574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.128669 restraints weight = 9760.285| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.54 r_work: 0.3972 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2161 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= 0.184 Angle : 0.503 6.256 6095 Z= 0.261 Chirality : 0.042 0.169 704 Planarity : 0.003 0.032 759 Dihedral : 7.947 71.576 647 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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 (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: -0.28 (0.36), residues: 558 helix: 1.31 (0.36), residues: 219 sheet: -1.04 (0.46), residues: 129 loop : -1.15 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.005 0.001 HIS A 396 PHE 0.007 0.001 PHE B 498 TYR 0.011 0.001 TYR A 436 ARG 0.005 0.001 ARG A 237 *********************** 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 54 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.492 Fit side-chains REVERT: A 503 MET cc_start: 0.8199 (mmt) cc_final: 0.7953 (mmp) REVERT: B 351 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8459 (mt) outliers start: 16 outliers final: 11 residues processed: 53 average time/residue: 0.4203 time to fit residues: 24.9498 Evaluate side-chains 46 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 226 ILE Chi-restraints excluded: chain B residue 351 LEU 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 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 6 optimal weight: 0.0470 chunk 35 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4214 r_free = 0.4214 target = 0.139046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.128133 restraints weight = 9447.924| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.50 r_work: 0.3971 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2186 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= 0.210 Angle : 0.547 7.046 6095 Z= 0.276 Chirality : 0.043 0.165 704 Planarity : 0.003 0.034 759 Dihedral : 7.985 71.793 647 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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 (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: -0.33 (0.37), residues: 558 helix: 1.25 (0.37), residues: 219 sheet: -1.11 (0.46), residues: 129 loop : -1.12 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.005 0.001 HIS A 396 PHE 0.009 0.001 PHE B 327 TYR 0.014 0.001 TYR A 436 ARG 0.005 0.001 ARG A 237 ********************** 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 46 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.538 Fit side-chains REVERT: A 503 MET cc_start: 0.8229 (mmt) cc_final: 0.7880 (mmm) REVERT: B 351 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8472 (mt) outliers start: 12 outliers final: 11 residues processed: 45 average time/residue: 0.4441 time to fit residues: 22.5564 Evaluate side-chains 45 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 226 ILE Chi-restraints excluded: chain B residue 351 LEU 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 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4189 r_free = 0.4189 target = 0.137038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126019 restraints weight = 9568.611| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.53 r_work: 0.3938 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4448 Z= 0.276 Angle : 0.575 6.823 6095 Z= 0.294 Chirality : 0.044 0.155 704 Planarity : 0.003 0.035 759 Dihedral : 8.209 73.135 647 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.21 % Allowed : 28.61 % 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 (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: -0.54 (0.37), residues: 558 helix: 1.09 (0.37), residues: 220 sheet: -1.27 (0.46), residues: 129 loop : -1.22 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.002 0.001 HIS A 457 PHE 0.011 0.001 PHE B 459 TYR 0.017 0.001 TYR A 436 ARG 0.004 0.001 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2264.44 seconds wall clock time: 41 minutes 15.57 seconds (2475.57 seconds total)