Starting phenix.real_space_refine on Thu Mar 13 12:52:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2d_17361/03_2025/8p2d_17361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2d_17361/03_2025/8p2d_17361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p2d_17361/03_2025/8p2d_17361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2d_17361/03_2025/8p2d_17361.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2d_17361/03_2025/8p2d_17361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2d_17361/03_2025/8p2d_17361.cif" } resolution = 2.59 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5555 2.51 5 N 1511 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8793 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4358 Classifications: {'peptide': 542} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 521} Chain breaks: 2 Chain: "B" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4373 Classifications: {'peptide': 545} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.97, per 1000 atoms: 0.68 Number of scatterers: 8793 At special positions: 0 Unit cell: (77.0224, 118.496, 95.6432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1665 8.00 N 1511 7.00 C 5555 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 47.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 121 through 141 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 196 through 213 Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.600A pdb=" N GLU A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.655A pdb=" N ALA A 257 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.583A pdb=" N THR A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 322 through 339 removed outlier: 4.280A pdb=" N ILE A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.914A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 455 through 486 removed outlier: 3.838A pdb=" N ARG A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.826A pdb=" N PHE A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.711A pdb=" N GLY A 520 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.609A pdb=" N CYS A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.844A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 587 through 595 removed outlier: 4.046A pdb=" N PHE A 595 " --> pdb=" O ASP A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.734A pdb=" N LYS A 624 " --> pdb=" O THR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.259A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.748A pdb=" N TYR A 666 " --> pdb=" O MET A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 142 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 144 through 152 removed outlier: 3.663A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 175 through 182 removed outlier: 4.224A pdb=" N ILE B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 4.165A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.810A pdb=" N SER B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.825A pdb=" N LEU B 246 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 278 through 301 removed outlier: 3.512A pdb=" N THR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.574A pdb=" N LEU B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.706A pdb=" N GLN B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.959A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.643A pdb=" N GLU B 410 " --> pdb=" O TYR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 455 through 486 removed outlier: 3.637A pdb=" N ARG B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 544 through 570 removed outlier: 3.774A pdb=" N GLN B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 591 Processing helix chain 'B' and resid 620 through 629 removed outlier: 3.661A pdb=" N LYS B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 653 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158 removed outlier: 5.145A pdb=" N ASN A 435 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLY A 523 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER A 437 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLY A 525 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE A 527 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 441 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 522 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 576 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 524 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.432A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 316 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN A 351 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU A 387 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TRP A 353 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 4.932A pdb=" N ASN B 435 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLY B 523 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER B 437 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLY B 525 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 439 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE B 527 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 441 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 522 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 576 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE B 524 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 221 removed outlier: 6.665A pdb=" N ILE B 221 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 315 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS B 354 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 317 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN B 351 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 387 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TRP B 353 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 642 through 643 312 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2887 1.34 - 1.46: 1546 1.46 - 1.57: 4457 1.57 - 1.69: 9 1.69 - 1.81: 90 Bond restraints: 8989 Sorted by residual: bond pdb=" C LYS B 508 " pdb=" N PRO B 509 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.08e-02 8.57e+03 1.76e+00 bond pdb=" C ILE B 221 " pdb=" O ILE B 221 " ideal model delta sigma weight residual 1.232 1.243 -0.011 1.01e-02 9.80e+03 1.29e+00 bond pdb=" C LYS A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.336 1.347 -0.011 1.08e-02 8.57e+03 9.90e-01 bond pdb=" CB PHE A 493 " pdb=" CG PHE A 493 " ideal model delta sigma weight residual 1.502 1.522 -0.020 2.30e-02 1.89e+03 7.54e-01 bond pdb=" CA SER B 304 " pdb=" C SER B 304 " ideal model delta sigma weight residual 1.528 1.516 0.011 1.33e-02 5.65e+03 7.31e-01 ... (remaining 8984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 11872 1.40 - 2.80: 236 2.80 - 4.19: 34 4.19 - 5.59: 10 5.59 - 6.99: 2 Bond angle restraints: 12154 Sorted by residual: angle pdb=" N LEU B 536 " pdb=" CA LEU B 536 " pdb=" C LEU B 536 " ideal model delta sigma weight residual 114.56 110.46 4.10 1.27e+00 6.20e-01 1.04e+01 angle pdb=" C ASP B 605 " pdb=" CA ASP B 605 " pdb=" CB ASP B 605 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.59e+00 angle pdb=" N ILE B 281 " pdb=" CA ILE B 281 " pdb=" C ILE B 281 " ideal model delta sigma weight residual 112.35 108.50 3.85 1.41e+00 5.03e-01 7.45e+00 angle pdb=" N ILE B 179 " pdb=" CA ILE B 179 " pdb=" C ILE B 179 " ideal model delta sigma weight residual 113.07 109.75 3.32 1.36e+00 5.41e-01 5.96e+00 angle pdb=" C HIS A 289 " pdb=" N GLN A 290 " pdb=" CA GLN A 290 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 ... (remaining 12149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 5137 21.57 - 43.14: 215 43.14 - 64.70: 51 64.70 - 86.27: 6 86.27 - 107.84: 3 Dihedral angle restraints: 5412 sinusoidal: 2247 harmonic: 3165 Sorted by residual: dihedral pdb=" CA TYR B 231 " pdb=" C TYR B 231 " pdb=" N VAL B 232 " pdb=" CA VAL B 232 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU A 511 " pdb=" C GLU A 511 " pdb=" N THR A 512 " pdb=" CA THR A 512 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR A 231 " pdb=" C TYR A 231 " pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 750 0.030 - 0.060: 378 0.060 - 0.090: 111 0.090 - 0.120: 52 0.120 - 0.150: 9 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ILE A 524 " pdb=" N ILE A 524 " pdb=" C ILE A 524 " pdb=" CB ILE A 524 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE B 524 " pdb=" N ILE B 524 " pdb=" C ILE B 524 " pdb=" CB ILE B 524 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL A 613 " pdb=" N VAL A 613 " pdb=" C VAL A 613 " pdb=" CB VAL A 613 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1297 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 290 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C GLN A 290 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN A 290 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 291 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 578 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO A 579 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 192 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 193 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.016 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 68 2.55 - 3.14: 6895 3.14 - 3.73: 13907 3.73 - 4.31: 19515 4.31 - 4.90: 31997 Nonbonded interactions: 72382 Sorted by model distance: nonbonded pdb=" O3G DTP A 801 " pdb="MG MG B 801 " model vdw 1.968 2.170 nonbonded pdb=" O3G DTP A 802 " pdb="MG MG A 803 " model vdw 1.989 2.170 nonbonded pdb=" OE2 GLU B 293 " pdb="MG MG B 801 " model vdw 2.160 2.170 nonbonded pdb=" OD2 ASP B 591 " pdb=" OH TYR B 607 " model vdw 2.249 3.040 nonbonded pdb=" NZ LYS A 241 " pdb=" O LEU A 251 " model vdw 2.254 3.120 ... (remaining 72377 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 120 through 674 or resid 803)) selection = (chain 'B' and (resid 120 through 302 or resid 311 through 674 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.120 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8989 Z= 0.154 Angle : 0.514 6.990 12154 Z= 0.286 Chirality : 0.042 0.150 1300 Planarity : 0.003 0.031 1569 Dihedral : 12.793 107.837 3382 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.79 % Allowed : 8.73 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1075 helix: -0.17 (0.25), residues: 487 sheet: 0.52 (0.48), residues: 111 loop : -2.42 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 501 HIS 0.002 0.001 HIS B 216 PHE 0.018 0.001 PHE B 224 TYR 0.011 0.001 TYR B 231 ARG 0.002 0.000 ARG B 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7016 (t0) cc_final: 0.6631 (m-40) REVERT: A 595 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: B 127 MET cc_start: 0.6589 (mmt) cc_final: 0.5050 (mpp) REVERT: B 409 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.6265 (m100) outliers start: 45 outliers final: 7 residues processed: 212 average time/residue: 1.1482 time to fit residues: 260.8051 Evaluate side-chains 157 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 483 GLN A 548 GLN A 611 ASN A 652 ASN B 153 HIS B 154 ASN B 188 HIS B 219 GLN B 237 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 334 GLN B 483 GLN B 541 HIS B 609 ASN B 652 ASN B 667 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.193452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.183115 restraints weight = 12071.895| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 1.61 r_work: 0.4338 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8989 Z= 0.199 Angle : 0.578 7.549 12154 Z= 0.309 Chirality : 0.044 0.210 1300 Planarity : 0.004 0.034 1569 Dihedral : 10.060 99.891 1267 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.58 % Allowed : 13.84 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 1075 helix: -0.02 (0.25), residues: 499 sheet: 0.34 (0.46), residues: 112 loop : -2.54 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 501 HIS 0.005 0.001 HIS A 541 PHE 0.024 0.002 PHE B 438 TYR 0.014 0.002 TYR B 617 ARG 0.007 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASP cc_start: 0.5946 (m-30) cc_final: 0.5712 (m-30) REVERT: A 595 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.5580 (m-80) REVERT: A 673 VAL cc_start: 0.6767 (p) cc_final: 0.6554 (m) REVERT: B 241 LYS cc_start: 0.4112 (mmpt) cc_final: 0.3510 (mmpt) REVERT: B 355 LYS cc_start: 0.8063 (tttp) cc_final: 0.7545 (tttt) REVERT: B 472 ASP cc_start: 0.5423 (t0) cc_final: 0.5190 (t70) REVERT: B 513 ILE cc_start: 0.4119 (OUTLIER) cc_final: 0.3437 (pt) outliers start: 43 outliers final: 12 residues processed: 192 average time/residue: 1.1077 time to fit residues: 228.1659 Evaluate side-chains 165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 153 HIS B 213 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.193558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.183699 restraints weight = 12156.323| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.53 r_work: 0.4336 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4223 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8989 Z= 0.197 Angle : 0.577 6.577 12154 Z= 0.305 Chirality : 0.044 0.209 1300 Planarity : 0.004 0.033 1569 Dihedral : 9.351 86.911 1259 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.15 % Allowed : 15.34 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1075 helix: 0.10 (0.25), residues: 493 sheet: 0.17 (0.46), residues: 112 loop : -2.51 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 501 HIS 0.003 0.001 HIS B 541 PHE 0.022 0.002 PHE B 438 TYR 0.015 0.001 TYR B 617 ARG 0.007 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5477 (m-80) REVERT: B 241 LYS cc_start: 0.4414 (mmpt) cc_final: 0.3993 (mmpt) REVERT: B 355 LYS cc_start: 0.8050 (tttp) cc_final: 0.7788 (tttt) REVERT: B 472 ASP cc_start: 0.5585 (t0) cc_final: 0.5243 (t0) REVERT: B 513 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3312 (pt) outliers start: 39 outliers final: 12 residues processed: 182 average time/residue: 1.1239 time to fit residues: 219.4256 Evaluate side-chains 167 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 435 ASN B 153 HIS B 213 ASN B 219 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 485 GLN B 541 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.194226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.184370 restraints weight = 12024.090| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.52 r_work: 0.4343 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4232 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8989 Z= 0.187 Angle : 0.564 6.852 12154 Z= 0.299 Chirality : 0.043 0.137 1300 Planarity : 0.004 0.032 1569 Dihedral : 8.573 84.992 1259 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.05 % Allowed : 17.89 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.25), residues: 1075 helix: 0.23 (0.25), residues: 494 sheet: 0.15 (0.46), residues: 112 loop : -2.46 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 501 HIS 0.003 0.001 HIS B 216 PHE 0.019 0.002 PHE B 438 TYR 0.021 0.001 TYR A 371 ARG 0.005 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5327 (m-80) REVERT: B 277 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5840 (mm-30) REVERT: B 355 LYS cc_start: 0.8043 (tttp) cc_final: 0.7645 (tttt) REVERT: B 472 ASP cc_start: 0.5513 (t0) cc_final: 0.5212 (t0) outliers start: 38 outliers final: 14 residues processed: 179 average time/residue: 1.5936 time to fit residues: 305.7276 Evaluate side-chains 164 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 480 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 chunk 35 optimal weight: 0.0070 chunk 44 optimal weight: 0.0040 chunk 48 optimal weight: 0.0050 chunk 22 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.0236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 298 ASN A 435 ASN B 153 HIS B 213 ASN B 219 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 334 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.199234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.189256 restraints weight = 12223.085| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 1.56 r_work: 0.4395 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4284 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8989 Z= 0.146 Angle : 0.538 7.312 12154 Z= 0.283 Chirality : 0.042 0.155 1300 Planarity : 0.003 0.040 1569 Dihedral : 7.282 67.267 1255 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.51 % Allowed : 18.85 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1075 helix: 0.53 (0.25), residues: 489 sheet: 0.11 (0.49), residues: 113 loop : -2.32 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 501 HIS 0.003 0.001 HIS B 541 PHE 0.017 0.001 PHE B 438 TYR 0.028 0.001 TYR A 164 ARG 0.009 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 MET cc_start: 0.6110 (mmm) cc_final: 0.5795 (tpp) REVERT: A 595 PHE cc_start: 0.6295 (OUTLIER) cc_final: 0.5332 (m-80) REVERT: A 673 VAL cc_start: 0.6444 (p) cc_final: 0.6226 (m) REVERT: B 153 HIS cc_start: 0.6914 (m90) cc_final: 0.6535 (m90) REVERT: B 277 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5515 (mm-30) REVERT: B 489 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6798 (mmt) outliers start: 33 outliers final: 9 residues processed: 169 average time/residue: 1.2471 time to fit residues: 226.1284 Evaluate side-chains 150 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 489 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 395 GLN B 213 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 334 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.194349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.183812 restraints weight = 12078.193| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 1.60 r_work: 0.4338 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4223 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8989 Z= 0.246 Angle : 0.617 8.316 12154 Z= 0.326 Chirality : 0.046 0.184 1300 Planarity : 0.004 0.046 1569 Dihedral : 7.722 73.567 1255 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.19 % Allowed : 20.13 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.25), residues: 1075 helix: 0.36 (0.25), residues: 487 sheet: -0.09 (0.47), residues: 111 loop : -2.41 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 501 HIS 0.008 0.001 HIS A 297 PHE 0.018 0.002 PHE B 224 TYR 0.022 0.002 TYR A 164 ARG 0.010 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5387 (m-80) REVERT: A 673 VAL cc_start: 0.6804 (p) cc_final: 0.6551 (m) REVERT: B 153 HIS cc_start: 0.7393 (m90) cc_final: 0.7020 (m90) REVERT: B 277 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5596 (mm-30) REVERT: B 319 THR cc_start: 0.7667 (t) cc_final: 0.7455 (m) outliers start: 30 outliers final: 14 residues processed: 176 average time/residue: 1.1373 time to fit residues: 215.6667 Evaluate side-chains 164 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.0070 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 395 GLN A 435 ASN B 213 ASN B 219 GLN B 278 GLN B 334 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.194323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.183877 restraints weight = 12245.285| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.60 r_work: 0.4341 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8989 Z= 0.232 Angle : 0.618 8.409 12154 Z= 0.326 Chirality : 0.045 0.189 1300 Planarity : 0.004 0.031 1569 Dihedral : 7.949 77.332 1251 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.62 % Allowed : 21.30 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.25), residues: 1075 helix: 0.32 (0.24), residues: 483 sheet: -0.18 (0.46), residues: 111 loop : -2.49 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 501 HIS 0.006 0.001 HIS B 541 PHE 0.016 0.002 PHE B 224 TYR 0.019 0.002 TYR A 164 ARG 0.008 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7604 (m-80) cc_final: 0.7231 (m-80) REVERT: A 433 ARG cc_start: 0.7252 (mtm-85) cc_final: 0.7041 (mtp-110) REVERT: A 595 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.5363 (m-80) REVERT: A 673 VAL cc_start: 0.6818 (p) cc_final: 0.6596 (m) REVERT: B 277 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5729 (mm-30) REVERT: B 497 MET cc_start: 0.7057 (mmm) cc_final: 0.6826 (mmt) outliers start: 34 outliers final: 16 residues processed: 178 average time/residue: 1.0830 time to fit residues: 207.1689 Evaluate side-chains 167 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 71 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 153 HIS B 213 ASN B 219 GLN B 334 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.194320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.183981 restraints weight = 12213.908| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 1.57 r_work: 0.4339 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8989 Z= 0.229 Angle : 0.645 9.473 12154 Z= 0.337 Chirality : 0.046 0.167 1300 Planarity : 0.004 0.031 1569 Dihedral : 7.992 78.368 1251 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.56 % Allowed : 22.58 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.25), residues: 1075 helix: 0.27 (0.24), residues: 483 sheet: -0.16 (0.47), residues: 111 loop : -2.51 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.005 0.001 HIS A 297 PHE 0.015 0.002 PHE B 224 TYR 0.017 0.002 TYR A 164 ARG 0.008 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7647 (m-80) cc_final: 0.7295 (m-80) REVERT: A 595 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5345 (m-80) REVERT: B 489 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6712 (mmt) outliers start: 24 outliers final: 14 residues processed: 166 average time/residue: 1.1117 time to fit residues: 197.8926 Evaluate side-chains 162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 0.0670 chunk 63 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 213 ASN B 219 GLN B 278 GLN B 334 GLN B 342 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.193847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.183616 restraints weight = 12182.912| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 1.55 r_work: 0.4337 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8989 Z= 0.246 Angle : 0.668 12.670 12154 Z= 0.348 Chirality : 0.046 0.175 1300 Planarity : 0.004 0.048 1569 Dihedral : 8.146 82.117 1251 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.41 % Allowed : 22.15 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.25), residues: 1075 helix: 0.23 (0.24), residues: 482 sheet: -0.21 (0.47), residues: 111 loop : -2.52 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 501 HIS 0.006 0.001 HIS B 153 PHE 0.016 0.002 PHE B 224 TYR 0.023 0.002 TYR B 617 ARG 0.014 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7646 (m-80) cc_final: 0.7265 (m-80) REVERT: A 595 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.5427 (m-80) REVERT: B 355 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7811 (pptt) REVERT: B 489 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6750 (mmt) outliers start: 32 outliers final: 18 residues processed: 166 average time/residue: 1.2996 time to fit residues: 231.6653 Evaluate side-chains 160 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.0010 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS B 278 GLN B 334 GLN B 342 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.195513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.185486 restraints weight = 12156.300| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.53 r_work: 0.4359 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4249 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8989 Z= 0.198 Angle : 0.644 10.082 12154 Z= 0.336 Chirality : 0.045 0.173 1300 Planarity : 0.004 0.054 1569 Dihedral : 7.876 77.629 1251 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.56 % Allowed : 23.00 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.25), residues: 1075 helix: 0.18 (0.24), residues: 488 sheet: -0.18 (0.47), residues: 112 loop : -2.37 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 501 HIS 0.006 0.001 HIS B 153 PHE 0.014 0.001 PHE B 438 TYR 0.024 0.002 TYR B 617 ARG 0.013 0.000 ARG B 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7651 (m-80) cc_final: 0.7242 (m-80) REVERT: A 595 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.5424 (m-80) REVERT: B 241 LYS cc_start: 0.4067 (mmpt) cc_final: 0.3414 (mmpt) REVERT: B 277 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5469 (mm-30) REVERT: B 355 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7778 (pptt) REVERT: B 489 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6763 (mmt) outliers start: 24 outliers final: 18 residues processed: 159 average time/residue: 1.1855 time to fit residues: 202.0205 Evaluate side-chains 160 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 40 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 395 GLN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 219 GLN B 278 GLN B 342 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.197524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.187376 restraints weight = 12147.802| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 1.60 r_work: 0.4380 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4266 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8989 Z= 0.166 Angle : 0.609 9.423 12154 Z= 0.318 Chirality : 0.044 0.159 1300 Planarity : 0.004 0.052 1569 Dihedral : 7.502 68.076 1251 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.56 % Allowed : 23.22 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.25), residues: 1075 helix: 0.28 (0.24), residues: 491 sheet: -0.20 (0.47), residues: 113 loop : -2.32 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 501 HIS 0.006 0.001 HIS B 216 PHE 0.014 0.001 PHE B 438 TYR 0.023 0.001 TYR B 617 ARG 0.013 0.000 ARG B 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7442.09 seconds wall clock time: 129 minutes 20.69 seconds (7760.69 seconds total)