Starting phenix.real_space_refine on Sat Aug 23 01:14:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2d_17361/08_2025/8p2d_17361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2d_17361/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p2d_17361/08_2025/8p2d_17361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2d_17361/08_2025/8p2d_17361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p2d_17361/08_2025/8p2d_17361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2d_17361/08_2025/8p2d_17361.map" } 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-2.0-5787/lib/python3.9/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: 2.29, per 1000 atoms: 0.26 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: 0.84 Conformation dependent library (CDL) restraints added in 338.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.31 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: 1.45 Time building geometry restraints manager: 1.09 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 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.740 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.120 ------------------------------------------------------------------------------- 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= 0.121 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00235 ( 8989) covalent geometry : angle 0.51448 (12154) hydrogen bonds : bond 0.19434 ( 310) hydrogen bonds : angle 7.12226 ( 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 : 0.324 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: 0.5605 time to fit residues: 127.0308 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 : 0.328 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 298 ASN B 334 GLN B 483 GLN B 541 HIS B 609 ASN B 652 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.193266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.182827 restraints weight = 12050.616| |-----------------------------------------------------------------------------| 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: 0.6612 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8989 Z= 0.178 Angle : 0.614 7.297 12154 Z= 0.331 Chirality : 0.045 0.198 1300 Planarity : 0.005 0.044 1569 Dihedral : 10.280 105.908 1267 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.90 % Allowed : 13.74 % Favored : 81.36 % 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 aren not related in a simple way. whole: -1.61 (0.25), residues: 1075 helix: -0.04 (0.25), residues: 489 sheet: 0.33 (0.46), residues: 111 loop : -2.60 (0.26), residues: 475 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 0.004 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8989) covalent geometry : angle 0.61401 (12154) hydrogen bonds : bond 0.05230 ( 310) hydrogen bonds : angle 5.48299 ( 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 : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7671 (t0) cc_final: 0.7440 (t0) REVERT: A 595 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: A 673 VAL cc_start: 0.6797 (p) cc_final: 0.6590 (m) REVERT: B 241 LYS cc_start: 0.4346 (mmpt) cc_final: 0.3534 (mmpt) REVERT: B 355 LYS cc_start: 0.8095 (tttp) cc_final: 0.7754 (tttt) REVERT: B 472 ASP cc_start: 0.5476 (t0) cc_final: 0.5201 (t0) outliers start: 46 outliers final: 15 residues processed: 197 average time/residue: 0.5600 time to fit residues: 118.1608 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 : 0.328 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 58 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 188 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 385 ASN A 435 ASN B 153 HIS B 213 ASN B 219 GLN B 278 GLN B 300 ASN B 338 GLN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.191689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.181722 restraints weight = 12004.041| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 1.54 r_work: 0.4314 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8989 Z= 0.167 Angle : 0.615 8.203 12154 Z= 0.326 Chirality : 0.046 0.244 1300 Planarity : 0.004 0.032 1569 Dihedral : 10.008 98.465 1259 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.37 % Allowed : 15.76 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.25), residues: 1075 helix: -0.04 (0.25), residues: 491 sheet: 0.15 (0.46), residues: 111 loop : -2.62 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 330 TYR 0.020 0.002 TYR A 371 PHE 0.022 0.002 PHE B 438 TRP 0.009 0.001 TRP A 501 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8989) covalent geometry : angle 0.61529 (12154) hydrogen bonds : bond 0.04891 ( 310) hydrogen bonds : angle 5.30943 ( 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 200 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7771 (t0) cc_final: 0.7550 (t0) REVERT: A 316 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.7112 (p0) REVERT: A 595 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5595 (m-80) REVERT: A 673 VAL cc_start: 0.6794 (p) cc_final: 0.6581 (m) REVERT: B 241 LYS cc_start: 0.4537 (OUTLIER) cc_final: 0.3852 (mmpt) REVERT: B 277 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5791 (mm-30) REVERT: B 355 LYS cc_start: 0.8094 (tttp) cc_final: 0.7818 (tttt) REVERT: B 472 ASP cc_start: 0.5568 (t0) cc_final: 0.5360 (t70) REVERT: B 513 ILE cc_start: 0.4108 (OUTLIER) cc_final: 0.3428 (pt) outliers start: 41 outliers final: 14 residues processed: 188 average time/residue: 0.5365 time to fit residues: 108.4460 Evaluate side-chains 168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU 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 462 MET 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 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 16 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 278 GLN B 300 ASN B 334 GLN ** B 541 HIS ** 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 = 0.4492 r_free = 0.4492 target = 0.192254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.182143 restraints weight = 12191.948| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 1.56 r_work: 0.4324 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4208 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8989 Z= 0.158 Angle : 0.598 7.054 12154 Z= 0.319 Chirality : 0.045 0.205 1300 Planarity : 0.004 0.039 1569 Dihedral : 9.639 90.468 1259 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.69 % Allowed : 17.47 % 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 aren not related in a simple way. whole: -1.61 (0.25), residues: 1075 helix: 0.05 (0.25), residues: 489 sheet: 0.04 (0.46), residues: 112 loop : -2.62 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 330 TYR 0.019 0.002 TYR A 164 PHE 0.019 0.002 PHE B 438 TRP 0.008 0.001 TRP A 501 HIS 0.004 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8989) covalent geometry : angle 0.59845 (12154) hydrogen bonds : bond 0.04649 ( 310) hydrogen bonds : angle 5.25189 ( 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 198 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7796 (t0) cc_final: 0.7569 (t0) REVERT: A 595 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.5627 (m-80) REVERT: A 673 VAL cc_start: 0.6837 (p) cc_final: 0.6625 (m) REVERT: B 140 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: B 277 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5739 (mm-30) REVERT: B 355 LYS cc_start: 0.8091 (tttp) cc_final: 0.7633 (tttt) REVERT: B 513 ILE cc_start: 0.3952 (OUTLIER) cc_final: 0.3262 (pt) outliers start: 44 outliers final: 18 residues processed: 183 average time/residue: 0.5902 time to fit residues: 115.6805 Evaluate side-chains 171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 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 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 575 ILE 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 169 LEU 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 390 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 B 153 HIS B 213 ASN B 278 GLN B 334 GLN ** 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 = 0.4508 r_free = 0.4508 target = 0.193645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.183586 restraints weight = 12258.766| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 1.55 r_work: 0.4339 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4227 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2369 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= 0.140 Angle : 0.586 7.313 12154 Z= 0.310 Chirality : 0.044 0.143 1300 Planarity : 0.004 0.032 1569 Dihedral : 9.180 90.683 1257 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.58 % Allowed : 18.42 % Favored : 77.00 % 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 aren not related in a simple way. whole: -1.50 (0.25), residues: 1075 helix: 0.17 (0.25), residues: 488 sheet: -0.08 (0.46), residues: 112 loop : -2.54 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 330 TYR 0.022 0.002 TYR A 164 PHE 0.017 0.002 PHE B 438 TRP 0.006 0.001 TRP A 501 HIS 0.003 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8989) covalent geometry : angle 0.58612 (12154) hydrogen bonds : bond 0.04264 ( 310) hydrogen bonds : angle 5.15914 ( 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 201 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7364 (mtm110) cc_final: 0.7154 (mpp-170) REVERT: A 300 ASN cc_start: 0.7750 (t0) cc_final: 0.7517 (t0) REVERT: A 433 ARG cc_start: 0.7142 (mtm-85) cc_final: 0.6892 (mtp180) REVERT: A 595 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5551 (m-80) REVERT: A 673 VAL cc_start: 0.6865 (OUTLIER) cc_final: 0.6616 (m) REVERT: B 241 LYS cc_start: 0.4583 (mmpt) cc_final: 0.4091 (mmpt) REVERT: B 277 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5750 (mm-30) REVERT: B 278 GLN cc_start: 0.5201 (OUTLIER) cc_final: 0.4815 (tt0) REVERT: B 355 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7718 (tttt) outliers start: 43 outliers final: 15 residues processed: 187 average time/residue: 0.5635 time to fit residues: 112.6777 Evaluate side-chains 175 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 537 ILE 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 140 ASP Chi-restraints excluded: chain B residue 160 ASP 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 513 ILE 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: 1.9990 chunk 99 optimal weight: 0.4980 chunk 33 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 213 ASN B 278 GLN B 334 GLN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.195894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.185698 restraints weight = 12218.105| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 1.56 r_work: 0.4360 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4248 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8989 Z= 0.114 Angle : 0.552 7.416 12154 Z= 0.292 Chirality : 0.043 0.142 1300 Planarity : 0.004 0.043 1569 Dihedral : 8.556 88.690 1257 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.47 % Allowed : 20.13 % Favored : 75.40 % 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 aren not related in a simple way. whole: -1.30 (0.26), residues: 1075 helix: 0.34 (0.25), residues: 489 sheet: -0.06 (0.47), residues: 112 loop : -2.42 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 330 TYR 0.016 0.001 TYR B 617 PHE 0.015 0.001 PHE B 438 TRP 0.005 0.001 TRP B 425 HIS 0.003 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8989) covalent geometry : angle 0.55201 (12154) hydrogen bonds : bond 0.03699 ( 310) hydrogen bonds : angle 5.00796 ( 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 194 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7294 (mtm110) cc_final: 0.7079 (mpp-170) REVERT: A 595 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5420 (m-80) REVERT: A 673 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6637 (m) REVERT: B 140 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6814 (OUTLIER) REVERT: B 241 LYS cc_start: 0.4453 (mmpt) cc_final: 0.4171 (mmpt) REVERT: B 277 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5457 (tp30) REVERT: B 278 GLN cc_start: 0.4993 (OUTLIER) cc_final: 0.4646 (tt0) REVERT: B 661 ASP cc_start: 0.7348 (m-30) cc_final: 0.7138 (m-30) outliers start: 42 outliers final: 13 residues processed: 179 average time/residue: 0.5799 time to fit residues: 111.2133 Evaluate side-chains 158 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 383 PHE Chi-restraints excluded: chain A residue 462 MET 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 140 ASP 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 312 PHE Chi-restraints excluded: chain B residue 480 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 213 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.194118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.184258 restraints weight = 12159.256| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.54 r_work: 0.4342 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4230 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.2685 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= 0.139 Angle : 0.583 8.093 12154 Z= 0.307 Chirality : 0.044 0.164 1300 Planarity : 0.004 0.032 1569 Dihedral : 8.381 91.385 1255 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.94 % Allowed : 21.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.25), residues: 1075 helix: 0.36 (0.25), residues: 488 sheet: -0.13 (0.46), residues: 111 loop : -2.47 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 330 TYR 0.024 0.002 TYR B 617 PHE 0.015 0.001 PHE B 438 TRP 0.005 0.001 TRP A 501 HIS 0.007 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8989) covalent geometry : angle 0.58317 (12154) hydrogen bonds : bond 0.03976 ( 310) hydrogen bonds : angle 5.08023 ( 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 180 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5366 (m-80) REVERT: B 277 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5710 (mm-30) REVERT: B 355 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7686 (tttt) outliers start: 37 outliers final: 17 residues processed: 168 average time/residue: 0.5561 time to fit residues: 99.9517 Evaluate side-chains 161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 225 ASP 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 355 LYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 537 ILE 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: 2.9990 chunk 45 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 153 HIS B 213 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.193060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.182808 restraints weight = 12106.434| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 1.57 r_work: 0.4333 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8989 Z= 0.170 Angle : 0.641 12.398 12154 Z= 0.335 Chirality : 0.046 0.168 1300 Planarity : 0.004 0.048 1569 Dihedral : 8.455 99.960 1255 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.83 % Allowed : 21.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.25), residues: 1075 helix: 0.33 (0.25), residues: 478 sheet: -0.19 (0.47), residues: 111 loop : -2.56 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 330 TYR 0.024 0.002 TYR B 617 PHE 0.015 0.002 PHE B 224 TRP 0.009 0.001 TRP A 501 HIS 0.006 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8989) covalent geometry : angle 0.64138 (12154) hydrogen bonds : bond 0.04472 ( 310) hydrogen bonds : angle 5.26775 ( 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 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7391 (m-80) cc_final: 0.7112 (m-80) REVERT: A 595 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: B 153 HIS cc_start: 0.7224 (m90) cc_final: 0.6963 (m90) REVERT: B 277 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5752 (mm-30) REVERT: B 355 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7571 (tttt) outliers start: 36 outliers final: 19 residues processed: 173 average time/residue: 0.5646 time to fit residues: 104.4927 Evaluate side-chains 167 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 0.0370 chunk 15 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 B 213 ASN B 278 GLN B 342 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.195505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.185323 restraints weight = 12139.135| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 1.56 r_work: 0.4362 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4249 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8989 Z= 0.127 Angle : 0.589 8.500 12154 Z= 0.311 Chirality : 0.044 0.169 1300 Planarity : 0.004 0.045 1569 Dihedral : 8.344 104.671 1255 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.98 % Allowed : 22.47 % 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 aren not related in a simple way. whole: -1.33 (0.25), residues: 1075 helix: 0.43 (0.25), residues: 483 sheet: -0.22 (0.47), residues: 112 loop : -2.51 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 330 TYR 0.024 0.001 TYR B 617 PHE 0.015 0.001 PHE B 438 TRP 0.011 0.001 TRP B 501 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8989) covalent geometry : angle 0.58853 (12154) hydrogen bonds : bond 0.03811 ( 310) hydrogen bonds : angle 5.04263 ( 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 169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7278 (m-80) cc_final: 0.7003 (m-80) REVERT: A 595 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5390 (m-80) REVERT: B 355 LYS cc_start: 0.7990 (tttp) cc_final: 0.7519 (tttt) REVERT: B 486 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6217 (pttp) outliers start: 28 outliers final: 19 residues processed: 163 average time/residue: 0.5861 time to fit residues: 102.1091 Evaluate side-chains 162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR 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 462 MET 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 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 476 LYS 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 537 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 37 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS 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 = 0.4534 r_free = 0.4534 target = 0.196001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.185851 restraints weight = 12210.384| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 1.56 r_work: 0.4370 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4258 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8989 Z= 0.130 Angle : 0.631 13.423 12154 Z= 0.326 Chirality : 0.045 0.201 1300 Planarity : 0.004 0.046 1569 Dihedral : 8.335 108.247 1255 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.24 % Allowed : 23.43 % Favored : 74.33 % 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 aren not related in a simple way. whole: -1.33 (0.25), residues: 1075 helix: 0.43 (0.25), residues: 482 sheet: -0.26 (0.46), residues: 112 loop : -2.50 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 330 TYR 0.023 0.001 TYR B 617 PHE 0.014 0.001 PHE B 438 TRP 0.011 0.001 TRP B 501 HIS 0.008 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8989) covalent geometry : angle 0.63120 (12154) hydrogen bonds : bond 0.03778 ( 310) hydrogen bonds : angle 5.07216 ( 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 160 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7232 (m-80) cc_final: 0.6989 (m-80) REVERT: A 595 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.5500 (m-80) REVERT: B 241 LYS cc_start: 0.4286 (mmpt) cc_final: 0.3875 (mmpt) REVERT: B 277 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5611 (mm-30) REVERT: B 355 LYS cc_start: 0.7979 (tttp) cc_final: 0.7500 (tttt) REVERT: B 486 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6195 (pttp) outliers start: 21 outliers final: 16 residues processed: 157 average time/residue: 0.5330 time to fit residues: 89.5130 Evaluate side-chains 155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 462 MET Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 595 PHE 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 476 LYS 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 537 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 101 optimal weight: 0.0770 chunk 107 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 278 GLN B 300 ASN 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 = 0.4522 r_free = 0.4522 target = 0.195834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.185804 restraints weight = 11978.970| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.52 r_work: 0.4355 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4242 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8989 Z= 0.160 Angle : 0.653 14.509 12154 Z= 0.340 Chirality : 0.046 0.255 1300 Planarity : 0.004 0.044 1569 Dihedral : 8.398 114.442 1255 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.88 % Allowed : 23.32 % Favored : 73.80 % 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 aren not related in a simple way. whole: -1.38 (0.25), residues: 1075 helix: 0.39 (0.25), residues: 476 sheet: -0.30 (0.46), residues: 112 loop : -2.49 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 330 TYR 0.023 0.002 TYR B 164 PHE 0.014 0.002 PHE B 224 TRP 0.009 0.001 TRP B 501 HIS 0.008 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8989) covalent geometry : angle 0.65305 (12154) hydrogen bonds : bond 0.04171 ( 310) hydrogen bonds : angle 5.12930 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.82 seconds wall clock time: 63 minutes 24.72 seconds (3804.72 seconds total)