Starting phenix.real_space_refine on Thu Jul 2 13:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p2d_17361/07_2026/8p2d_17361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2d_17361/07_2026/8p2d_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_17361/07_2026/8p2d_17361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2d_17361/07_2026/8p2d_17361.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8p2d_17361/07_2026/8p2d_17361.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p2d_17361/07_2026/8p2d_17361.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p2d_17361/07_2026/8p2d_17361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2d_17361/07_2026/8p2d_17361.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.24, per 1000 atoms: 0.25 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: 0.75 Conformation dependent library (CDL) restraints added in 441.5 milliseconds 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: 0.25 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: 1.30 Time building geometry restraints manager: 1.02 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: 5106 21.57 - 43.14: 205 43.14 - 64.70: 43 64.70 - 86.27: 2 86.27 - 107.84: 2 Dihedral angle restraints: 5358 sinusoidal: 2193 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 5355 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 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: 2.190 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.600 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 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= 0.121 Angle : 0.514 6.990 12154 Z= 0.286 Chirality : 0.042 0.150 1300 Planarity : 0.003 0.031 1569 Dihedral : 12.076 107.837 3328 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.002 0.000 ARG B 419 TYR 0.011 0.001 TYR B 231 PHE 0.018 0.001 PHE B 224 TRP 0.005 0.001 TRP B 501 HIS 0.002 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 8989) covalent geometry : angle 0.51448 / 0.29 (12154) hydrogen bonds : bond 0.19434 / 13.15 ( 310) hydrogen bonds : angle 7.12226 / 5.23 ( 900) *********************** 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 : 0.327 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: 0.5125 time to fit residues: 116.4902 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 : 0.319 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.0270 overall best weight: 0.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 300 ASN A 483 GLN A 548 GLN A 652 ASN B 153 HIS B 154 ASN B 188 HIS B 219 GLN B 237 GLN B 278 GLN B 297 HIS B 334 GLN B 483 GLN B 541 HIS B 609 ASN B 652 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.193251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.182807 restraints weight = 12050.838| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.61 r_work: 0.4320 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8989 Z= 0.178 Angle : 0.612 6.734 12154 Z= 0.330 Chirality : 0.045 0.184 1300 Planarity : 0.005 0.043 1569 Dihedral : 7.710 110.096 1213 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.90 % Allowed : 13.63 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.25), residues: 1075 helix: -0.06 (0.25), residues: 494 sheet: 0.26 (0.46), residues: 112 loop : -2.63 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 330 TYR 0.015 0.002 TYR B 616 PHE 0.025 0.002 PHE B 438 TRP 0.009 0.001 TRP A 501 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 8989) covalent geometry : angle 0.61155 / 0.33 (12154) hydrogen bonds : bond 0.05327 / 3.58 ( 310) hydrogen bonds : angle 5.49538 / 4.00 ( 900) *********************** 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 207 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7669 (t0) cc_final: 0.7435 (t0) REVERT: A 595 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5619 (m-80) REVERT: A 673 VAL cc_start: 0.6795 (p) cc_final: 0.6583 (m) REVERT: B 355 LYS cc_start: 0.8094 (tttp) cc_final: 0.7747 (tttt) outliers start: 46 outliers final: 15 residues processed: 196 average time/residue: 0.5104 time to fit residues: 107.4875 Evaluate side-chains 173 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 380 ARG 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 278 GLN 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 102 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 64 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 153 HIS B 213 ASN B 278 GLN B 300 ASN ** B 541 HIS ** 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 = 0.4505 r_free = 0.4505 target = 0.193483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.183728 restraints weight = 12039.946| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.52 r_work: 0.4337 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.1946 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= 0.131 Angle : 0.582 8.447 12154 Z= 0.306 Chirality : 0.044 0.200 1300 Planarity : 0.004 0.032 1569 Dihedral : 7.093 102.588 1205 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.37 % Allowed : 15.97 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.25), residues: 1075 helix: 0.03 (0.25), residues: 493 sheet: 0.13 (0.46), residues: 112 loop : -2.53 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.020 0.001 TYR A 371 PHE 0.021 0.001 PHE B 438 TRP 0.005 0.001 TRP A 501 HIS 0.003 0.001 HIS B 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8989) covalent geometry : angle 0.58180 / 0.31 (12154) hydrogen bonds : bond 0.04366 / 2.90 ( 310) hydrogen bonds : angle 5.15486 / 3.72 ( 900) *********************** 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 205 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: A 673 VAL cc_start: 0.6766 (p) cc_final: 0.6552 (m) REVERT: B 211 CYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7207 (t) REVERT: B 241 LYS cc_start: 0.4427 (OUTLIER) cc_final: 0.3989 (mmpt) REVERT: B 277 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5809 (mm-30) REVERT: B 355 LYS cc_start: 0.8090 (tttp) cc_final: 0.7811 (tttt) REVERT: B 497 MET cc_start: 0.7400 (mmm) cc_final: 0.7137 (mmm) outliers start: 41 outliers final: 12 residues processed: 189 average time/residue: 0.5041 time to fit residues: 102.4203 Evaluate side-chains 173 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 381 ARG Chi-restraints excluded: chain A residue 462 MET 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 241 LYS 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 476 LYS Chi-restraints excluded: chain B residue 480 GLU 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 16 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 103 optimal weight: 0.0670 chunk 82 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 435 ASN B 153 HIS B 213 ASN B 278 GLN B 300 ASN B 541 HIS B 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.194155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.184333 restraints weight = 12262.779| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.53 r_work: 0.4342 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4230 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8989 Z= 0.128 Angle : 0.569 7.125 12154 Z= 0.301 Chirality : 0.044 0.224 1300 Planarity : 0.004 0.039 1569 Dihedral : 6.955 99.109 1205 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.58 % Allowed : 17.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.25), residues: 1075 helix: 0.15 (0.25), residues: 497 sheet: 0.06 (0.46), residues: 112 loop : -2.54 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 330 TYR 0.019 0.001 TYR A 164 PHE 0.019 0.001 PHE B 438 TRP 0.006 0.001 TRP B 501 HIS 0.003 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8989) covalent geometry : angle 0.56897 / 0.30 (12154) hydrogen bonds : bond 0.04139 / 2.77 ( 310) hydrogen bonds : angle 5.07942 / 3.67 ( 900) *********************** 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 200 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5339 (m-80) REVERT: B 241 LYS cc_start: 0.4354 (OUTLIER) cc_final: 0.3911 (mmpt) REVERT: B 277 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5730 (mm-30) REVERT: B 355 LYS cc_start: 0.8081 (tttp) cc_final: 0.7655 (tttt) outliers start: 43 outliers final: 16 residues processed: 185 average time/residue: 0.5255 time to fit residues: 104.3205 Evaluate side-chains 169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 427 GLU 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 241 LYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 2 optimal weight: 0.0670 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 435 ASN A 674 ASN B 153 HIS B 213 ASN B 278 GLN B 300 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.193049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.183277 restraints weight = 12237.136| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.51 r_work: 0.4332 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8989 Z= 0.160 Angle : 0.603 7.714 12154 Z= 0.320 Chirality : 0.045 0.152 1300 Planarity : 0.004 0.041 1569 Dihedral : 6.910 99.787 1201 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.79 % Allowed : 18.96 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.25), residues: 1075 helix: 0.20 (0.25), residues: 488 sheet: -0.00 (0.47), residues: 111 loop : -2.54 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 330 TYR 0.029 0.002 TYR A 164 PHE 0.018 0.002 PHE B 438 TRP 0.009 0.001 TRP A 501 HIS 0.005 0.001 HIS B 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 8989) covalent geometry : angle 0.60345 / 0.32 (12154) hydrogen bonds : bond 0.04499 / 3.01 ( 310) hydrogen bonds : angle 5.17854 / 3.75 ( 900) *********************** 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 191 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7354 (mtm110) cc_final: 0.7111 (mpp-170) REVERT: A 595 PHE cc_start: 0.6301 (OUTLIER) cc_final: 0.5504 (m-80) REVERT: B 153 HIS cc_start: 0.7309 (m90) cc_final: 0.6962 (m90) REVERT: B 277 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5782 (mm-30) outliers start: 45 outliers final: 17 residues processed: 179 average time/residue: 0.5469 time to fit residues: 104.7079 Evaluate side-chains 162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 178 VAL 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 502 VAL Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 0.0170 chunk 99 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 213 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 334 GLN B 485 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.193701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.183598 restraints weight = 12222.454| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 1.56 r_work: 0.4338 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8989 Z= 0.151 Angle : 0.604 8.605 12154 Z= 0.319 Chirality : 0.045 0.146 1300 Planarity : 0.004 0.033 1569 Dihedral : 6.910 99.096 1201 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.26 % Allowed : 20.02 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.25), residues: 1075 helix: 0.20 (0.25), residues: 489 sheet: -0.10 (0.47), residues: 111 loop : -2.51 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 330 TYR 0.024 0.002 TYR A 164 PHE 0.016 0.001 PHE B 438 TRP 0.007 0.001 TRP A 501 HIS 0.004 0.001 HIS B 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8989) covalent geometry : angle 0.60391 / 0.32 (12154) hydrogen bonds : bond 0.04331 / 2.89 ( 310) hydrogen bonds : angle 5.20093 / 3.76 ( 900) *********************** 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 191 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7333 (mtm110) cc_final: 0.7075 (mpp-170) REVERT: A 595 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5371 (m-80) REVERT: B 241 LYS cc_start: 0.4416 (mmpt) cc_final: 0.3684 (mmpt) REVERT: B 277 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5748 (mm-30) REVERT: B 355 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7731 (tttt) outliers start: 40 outliers final: 20 residues processed: 177 average time/residue: 0.5421 time to fit residues: 102.7266 Evaluate side-chains 170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 169 LEU Chi-restraints excluded: chain B residue 178 VAL 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 355 LYS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 663 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 37 optimal weight: 0.0050 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 435 ASN B 212 GLN B 213 ASN B 278 GLN B 334 GLN ** 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 = 0.4517 r_free = 0.4517 target = 0.194733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.184747 restraints weight = 12155.131| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 1.53 r_work: 0.4348 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4236 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8989 Z= 0.135 Angle : 0.601 9.262 12154 Z= 0.313 Chirality : 0.044 0.162 1300 Planarity : 0.004 0.049 1569 Dihedral : 6.778 94.577 1201 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.51 % Allowed : 21.73 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.25), residues: 1075 helix: 0.29 (0.25), residues: 490 sheet: -0.13 (0.46), residues: 111 loop : -2.45 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 330 TYR 0.020 0.001 TYR A 164 PHE 0.015 0.001 PHE B 438 TRP 0.004 0.001 TRP A 501 HIS 0.005 0.001 HIS B 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8989) covalent geometry : angle 0.60075 / 0.31 (12154) hydrogen bonds : bond 0.03993 / 2.67 ( 310) hydrogen bonds : angle 5.09374 / 3.70 ( 900) *********************** 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 182 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7318 (mtm110) cc_final: 0.7032 (mpp-170) REVERT: A 595 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.5412 (m-80) REVERT: B 241 LYS cc_start: 0.4393 (mmpt) cc_final: 0.3721 (mmpt) REVERT: B 277 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5903 (mm-30) REVERT: B 355 LYS cc_start: 0.8048 (tttp) cc_final: 0.7699 (tttt) REVERT: B 661 ASP cc_start: 0.7386 (m-30) cc_final: 0.7128 (m-30) outliers start: 33 outliers final: 14 residues processed: 174 average time/residue: 0.5270 time to fit residues: 98.2480 Evaluate side-chains 158 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU 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 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 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 502 VAL 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 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 213 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 334 GLN ** 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 = 0.4503 r_free = 0.4503 target = 0.193050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.182856 restraints weight = 12067.755| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.56 r_work: 0.4329 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4215 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 0.043 8989 Z= 0.175 Angle : 0.658 11.149 12154 Z= 0.342 Chirality : 0.046 0.172 1300 Planarity : 0.004 0.055 1569 Dihedral : 7.062 100.874 1201 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.73 % Allowed : 21.73 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.25), residues: 1075 helix: 0.22 (0.24), residues: 488 sheet: -0.29 (0.46), residues: 111 loop : -2.51 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 330 TYR 0.025 0.002 TYR B 617 PHE 0.016 0.002 PHE B 224 TRP 0.009 0.001 TRP A 501 HIS 0.006 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 8989) covalent geometry : angle 0.65778 / 0.34 (12154) hydrogen bonds : bond 0.04529 / 3.03 ( 310) hydrogen bonds : angle 5.24218 / 3.81 ( 900) *********************** 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 182 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: B 212 GLN cc_start: 0.7510 (tp-100) cc_final: 0.7198 (tp-100) REVERT: B 241 LYS cc_start: 0.4535 (mmpt) cc_final: 0.3875 (mmpt) REVERT: B 277 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5904 (mm-30) outliers start: 35 outliers final: 21 residues processed: 170 average time/residue: 0.5235 time to fit residues: 95.2655 Evaluate side-chains 168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 A residue 673 VAL 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 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 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 537 ILE 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 9 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 89 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 213 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.194554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.184328 restraints weight = 12147.862| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.58 r_work: 0.4345 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4232 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8989 Z= 0.145 Angle : 0.636 12.598 12154 Z= 0.331 Chirality : 0.045 0.171 1300 Planarity : 0.004 0.053 1569 Dihedral : 6.945 98.375 1201 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.41 % Allowed : 22.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.25), residues: 1075 helix: 0.26 (0.24), residues: 488 sheet: -0.31 (0.46), residues: 111 loop : -2.47 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 330 TYR 0.025 0.002 TYR B 617 PHE 0.015 0.001 PHE B 438 TRP 0.005 0.001 TRP A 501 HIS 0.006 0.001 HIS B 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8989) covalent geometry : angle 0.63647 / 0.33 (12154) hydrogen bonds : bond 0.04096 / 2.73 ( 310) hydrogen bonds : angle 5.18413 / 3.76 ( 900) *********************** 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 176 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7241 (m-80) cc_final: 0.6914 (m-80) REVERT: A 595 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.5329 (m-80) REVERT: B 277 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5841 (mm-30) REVERT: B 486 LYS cc_start: 0.6760 (ttpt) cc_final: 0.6245 (pttp) outliers start: 32 outliers final: 22 residues processed: 168 average time/residue: 0.4959 time to fit residues: 89.2414 Evaluate side-chains 166 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 A residue 673 VAL 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 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 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 537 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 385 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 278 GLN B 342 ASN ** 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 = 0.4506 r_free = 0.4506 target = 0.193546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.183321 restraints weight = 12105.295| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 1.58 r_work: 0.4338 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8989 Z= 0.174 Angle : 0.671 10.294 12154 Z= 0.351 Chirality : 0.047 0.204 1300 Planarity : 0.004 0.058 1569 Dihedral : 7.059 97.851 1201 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.09 % Allowed : 23.00 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.25), residues: 1075 helix: 0.19 (0.24), residues: 488 sheet: -0.34 (0.46), residues: 112 loop : -2.49 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 330 TYR 0.023 0.002 TYR B 617 PHE 0.015 0.002 PHE B 224 TRP 0.009 0.001 TRP A 501 HIS 0.008 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8989) covalent geometry : angle 0.67139 / 0.35 (12154) hydrogen bonds : bond 0.04398 / 2.94 ( 310) hydrogen bonds : angle 5.27244 / 3.84 ( 900) ********************** 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 170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7311 (m-80) cc_final: 0.7039 (m-80) REVERT: A 595 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5397 (m-80) REVERT: B 241 LYS cc_start: 0.4181 (mmpt) cc_final: 0.3208 (mmpt) REVERT: B 277 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5940 (mm-30) REVERT: B 486 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6205 (pttp) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 0.4805 time to fit residues: 83.4109 Evaluate side-chains 162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 595 PHE Chi-restraints excluded: chain A residue 673 VAL 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 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 480 GLU Chi-restraints excluded: chain B residue 486 LYS Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 537 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.0980 chunk 101 optimal weight: 0.0070 chunk 107 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 213 ASN B 278 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 = 0.4518 r_free = 0.4518 target = 0.194863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.184687 restraints weight = 12017.065| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.56 r_work: 0.4354 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4240 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8989 Z= 0.144 Angle : 0.630 8.713 12154 Z= 0.330 Chirality : 0.045 0.170 1300 Planarity : 0.004 0.056 1569 Dihedral : 6.918 96.732 1201 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.77 % Allowed : 23.75 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.25), residues: 1075 helix: 0.35 (0.25), residues: 483 sheet: -0.34 (0.45), residues: 112 loop : -2.51 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 330 TYR 0.023 0.002 TYR B 617 PHE 0.014 0.001 PHE B 438 TRP 0.005 0.001 TRP A 501 HIS 0.006 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8989) covalent geometry : angle 0.63008 / 0.33 (12154) hydrogen bonds : bond 0.04000 / 2.66 ( 310) hydrogen bonds : angle 5.16287 / 3.75 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.82 seconds wall clock time: 61 minutes 4.82 seconds (3664.82 seconds total)