Starting phenix.real_space_refine on Mon May 12 10:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2d_17361/05_2025/8p2d_17361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2d_17361/05_2025/8p2d_17361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p2d_17361/05_2025/8p2d_17361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2d_17361/05_2025/8p2d_17361.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2d_17361/05_2025/8p2d_17361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2d_17361/05_2025/8p2d_17361.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5555 2.51 5 N 1511 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8793 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4358 Classifications: {'peptide': 542} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 521} Chain breaks: 2 Chain: "B" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4373 Classifications: {'peptide': 545} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.85, per 1000 atoms: 0.67 Number of scatterers: 8793 At special positions: 0 Unit cell: (77.0224, 118.496, 95.6432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1665 8.00 N 1511 7.00 C 5555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 947.6 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: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 121 through 141 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 196 through 213 Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.600A pdb=" N GLU A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.655A pdb=" N ALA A 257 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.583A pdb=" N THR A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 322 through 339 removed outlier: 4.280A pdb=" N ILE A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.914A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 455 through 486 removed outlier: 3.838A pdb=" N ARG A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.826A pdb=" N PHE A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.711A pdb=" N GLY A 520 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.609A pdb=" N CYS A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.844A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 587 through 595 removed outlier: 4.046A pdb=" N PHE A 595 " --> pdb=" O ASP A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.734A pdb=" N LYS A 624 " --> pdb=" O THR A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.259A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.748A pdb=" N TYR A 666 " --> pdb=" O MET A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 142 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 144 through 152 removed outlier: 3.663A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 175 through 182 removed outlier: 4.224A pdb=" N ILE B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 4.165A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.810A pdb=" N SER B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.825A pdb=" N LEU B 246 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 278 through 301 removed outlier: 3.512A pdb=" N THR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.574A pdb=" N LEU B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.706A pdb=" N GLN B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.959A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.643A pdb=" N GLU B 410 " --> pdb=" O TYR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 455 through 486 removed outlier: 3.637A pdb=" N ARG B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 544 through 570 removed outlier: 3.774A pdb=" N GLN B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 591 Processing helix chain 'B' and resid 620 through 629 removed outlier: 3.661A pdb=" N LYS B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 653 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158 removed outlier: 5.145A pdb=" N ASN A 435 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLY A 523 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER A 437 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLY A 525 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE A 527 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 441 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 522 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 576 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 524 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.432A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 316 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN A 351 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU A 387 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TRP A 353 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 4.932A pdb=" N ASN B 435 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLY B 523 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER B 437 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLY B 525 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 439 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE B 527 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 441 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 522 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 576 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE B 524 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 221 removed outlier: 6.665A pdb=" N ILE B 221 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 315 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS B 354 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 317 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN B 351 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 387 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TRP B 353 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 642 through 643 312 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2887 1.34 - 1.46: 1546 1.46 - 1.57: 4457 1.57 - 1.69: 9 1.69 - 1.81: 90 Bond restraints: 8989 Sorted by residual: bond pdb=" C LYS B 508 " pdb=" N PRO B 509 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.08e-02 8.57e+03 1.76e+00 bond pdb=" C ILE B 221 " pdb=" O ILE B 221 " ideal model delta sigma weight residual 1.232 1.243 -0.011 1.01e-02 9.80e+03 1.29e+00 bond pdb=" C LYS A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.336 1.347 -0.011 1.08e-02 8.57e+03 9.90e-01 bond pdb=" CB PHE A 493 " pdb=" CG PHE A 493 " ideal model delta sigma weight residual 1.502 1.522 -0.020 2.30e-02 1.89e+03 7.54e-01 bond pdb=" CA SER B 304 " pdb=" C SER B 304 " ideal model delta sigma weight residual 1.528 1.516 0.011 1.33e-02 5.65e+03 7.31e-01 ... (remaining 8984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 11872 1.40 - 2.80: 236 2.80 - 4.19: 34 4.19 - 5.59: 10 5.59 - 6.99: 2 Bond angle restraints: 12154 Sorted by residual: angle pdb=" N LEU B 536 " pdb=" CA LEU B 536 " pdb=" C LEU B 536 " ideal model delta sigma weight residual 114.56 110.46 4.10 1.27e+00 6.20e-01 1.04e+01 angle pdb=" C ASP B 605 " pdb=" CA ASP B 605 " pdb=" CB ASP B 605 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.59e+00 angle pdb=" N ILE B 281 " pdb=" CA ILE B 281 " pdb=" C ILE B 281 " ideal model delta sigma weight residual 112.35 108.50 3.85 1.41e+00 5.03e-01 7.45e+00 angle pdb=" N ILE B 179 " pdb=" CA ILE B 179 " pdb=" C ILE B 179 " ideal model delta sigma weight residual 113.07 109.75 3.32 1.36e+00 5.41e-01 5.96e+00 angle pdb=" C HIS A 289 " pdb=" N GLN A 290 " pdb=" CA GLN A 290 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 ... (remaining 12149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 5137 21.57 - 43.14: 215 43.14 - 64.70: 51 64.70 - 86.27: 6 86.27 - 107.84: 3 Dihedral angle restraints: 5412 sinusoidal: 2247 harmonic: 3165 Sorted by residual: dihedral pdb=" CA TYR B 231 " pdb=" C TYR B 231 " pdb=" N VAL B 232 " pdb=" CA VAL B 232 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU A 511 " pdb=" C GLU A 511 " pdb=" N THR A 512 " pdb=" CA THR A 512 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR A 231 " pdb=" C TYR A 231 " pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 750 0.030 - 0.060: 378 0.060 - 0.090: 111 0.090 - 0.120: 52 0.120 - 0.150: 9 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ILE A 524 " pdb=" N ILE A 524 " pdb=" C ILE A 524 " pdb=" CB ILE A 524 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE B 524 " pdb=" N ILE B 524 " pdb=" C ILE B 524 " pdb=" CB ILE B 524 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL A 613 " pdb=" N VAL A 613 " pdb=" C VAL A 613 " pdb=" CB VAL A 613 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1297 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 290 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C GLN A 290 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN A 290 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 291 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 578 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO A 579 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 192 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 193 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.016 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 68 2.55 - 3.14: 6895 3.14 - 3.73: 13907 3.73 - 4.31: 19515 4.31 - 4.90: 31997 Nonbonded interactions: 72382 Sorted by model distance: nonbonded pdb=" O3G DTP A 801 " pdb="MG MG B 801 " model vdw 1.968 2.170 nonbonded pdb=" O3G DTP A 802 " pdb="MG MG A 803 " model vdw 1.989 2.170 nonbonded pdb=" OE2 GLU B 293 " pdb="MG MG B 801 " model vdw 2.160 2.170 nonbonded pdb=" OD2 ASP B 591 " pdb=" OH TYR B 607 " model vdw 2.249 3.040 nonbonded pdb=" NZ LYS A 241 " pdb=" O LEU A 251 " model vdw 2.254 3.120 ... (remaining 72377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 120 through 674 or resid 803)) selection = (chain 'B' and (resid 120 through 302 or resid 311 through 674 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.320 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.560 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.26), residues: 1075 helix: -0.17 (0.25), residues: 487 sheet: 0.52 (0.48), residues: 111 loop : -2.42 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 501 HIS 0.002 0.001 HIS B 216 PHE 0.018 0.001 PHE B 224 TYR 0.011 0.001 TYR B 231 ARG 0.002 0.000 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.19434 ( 310) hydrogen bonds : angle 7.12226 ( 900) covalent geometry : bond 0.00235 ( 8989) covalent geometry : angle 0.51448 (12154) *********************** 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 : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7016 (t0) cc_final: 0.6631 (m-40) REVERT: A 595 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: B 127 MET cc_start: 0.6589 (mmt) cc_final: 0.5050 (mpp) REVERT: B 409 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.6265 (m100) outliers start: 45 outliers final: 7 residues processed: 212 average time/residue: 1.0648 time to fit residues: 242.0885 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 : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 483 GLN A 548 GLN A 611 ASN A 652 ASN B 153 HIS B 154 ASN B 188 HIS B 219 GLN B 237 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 334 GLN B 483 GLN B 541 HIS B 609 ASN B 652 ASN B 667 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.193452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.183114 restraints weight = 12071.895| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 1.61 r_work: 0.4338 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8989 Z= 0.142 Angle : 0.578 7.549 12154 Z= 0.309 Chirality : 0.044 0.210 1300 Planarity : 0.004 0.034 1569 Dihedral : 10.060 99.891 1267 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.58 % Allowed : 13.84 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 1075 helix: -0.02 (0.25), residues: 499 sheet: 0.34 (0.46), residues: 112 loop : -2.54 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 501 HIS 0.005 0.001 HIS A 541 PHE 0.024 0.002 PHE B 438 TYR 0.014 0.002 TYR B 617 ARG 0.007 0.000 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 310) hydrogen bonds : angle 5.37787 ( 900) covalent geometry : bond 0.00303 ( 8989) covalent geometry : angle 0.57764 (12154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASP cc_start: 0.5948 (m-30) cc_final: 0.5713 (m-30) REVERT: A 595 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.5577 (m-80) REVERT: A 673 VAL cc_start: 0.6764 (p) cc_final: 0.6552 (m) REVERT: B 241 LYS cc_start: 0.4111 (mmpt) cc_final: 0.3510 (mmpt) REVERT: B 355 LYS cc_start: 0.8063 (tttp) cc_final: 0.7545 (tttt) REVERT: B 472 ASP cc_start: 0.5426 (t0) cc_final: 0.5193 (t70) REVERT: B 513 ILE cc_start: 0.4120 (OUTLIER) cc_final: 0.3441 (pt) outliers start: 43 outliers final: 12 residues processed: 192 average time/residue: 1.1091 time to fit residues: 228.6900 Evaluate side-chains 165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 153 HIS B 213 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN 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 = 0.4503 r_free = 0.4503 target = 0.193301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.183413 restraints weight = 12144.694| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 1.53 r_work: 0.4333 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8989 Z= 0.142 Angle : 0.582 6.659 12154 Z= 0.308 Chirality : 0.045 0.211 1300 Planarity : 0.004 0.035 1569 Dihedral : 9.405 88.003 1259 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.26 % Allowed : 15.34 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.25), residues: 1075 helix: 0.08 (0.25), residues: 493 sheet: 0.14 (0.46), residues: 112 loop : -2.51 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 501 HIS 0.003 0.001 HIS A 188 PHE 0.022 0.002 PHE B 438 TYR 0.015 0.001 TYR B 617 ARG 0.008 0.000 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 310) hydrogen bonds : angle 5.16341 ( 900) covalent geometry : bond 0.00306 ( 8989) covalent geometry : angle 0.58199 (12154) *********************** 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 201 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.5511 (m-80) REVERT: B 241 LYS cc_start: 0.4435 (OUTLIER) cc_final: 0.3996 (mmpt) REVERT: B 355 LYS cc_start: 0.8053 (tttp) cc_final: 0.7795 (tttt) REVERT: B 472 ASP cc_start: 0.5583 (t0) cc_final: 0.5246 (t0) REVERT: B 513 ILE cc_start: 0.4020 (OUTLIER) cc_final: 0.3334 (pt) outliers start: 40 outliers final: 13 residues processed: 185 average time/residue: 1.0884 time to fit residues: 216.0441 Evaluate side-chains 171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 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 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 300 ASN A 435 ASN B 153 HIS B 213 ASN B 219 GLN B 278 GLN B 300 ASN B 541 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.191944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.181957 restraints weight = 11990.983| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.53 r_work: 0.4322 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4208 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2180 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= 0.177 Angle : 0.613 7.033 12154 Z= 0.328 Chirality : 0.046 0.140 1300 Planarity : 0.004 0.032 1569 Dihedral : 9.075 88.124 1259 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.69 % Allowed : 17.57 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.25), residues: 1075 helix: 0.10 (0.25), residues: 487 sheet: 0.08 (0.46), residues: 111 loop : -2.54 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 501 HIS 0.004 0.001 HIS B 157 PHE 0.020 0.002 PHE B 438 TYR 0.022 0.002 TYR A 371 ARG 0.006 0.000 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 310) hydrogen bonds : angle 5.29504 ( 900) covalent geometry : bond 0.00392 ( 8989) covalent geometry : angle 0.61262 (12154) *********************** 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 201 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7351 (mpp-170) cc_final: 0.7109 (mtm110) REVERT: A 300 ASN cc_start: 0.7805 (t0) cc_final: 0.7604 (t0) REVERT: A 595 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5543 (m-80) REVERT: B 241 LYS cc_start: 0.4709 (OUTLIER) cc_final: 0.4349 (mmpt) REVERT: B 277 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5495 (mm-30) REVERT: B 355 LYS cc_start: 0.8074 (tttp) cc_final: 0.7802 (tttt) outliers start: 44 outliers final: 17 residues processed: 186 average time/residue: 1.1023 time to fit residues: 219.9885 Evaluate side-chains 169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 575 ILE 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 390 ASP Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 0.0060 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 300 ASN 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 = 0.4503 r_free = 0.4503 target = 0.193462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.183488 restraints weight = 12114.826| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.53 r_work: 0.4333 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2374 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= 0.141 Angle : 0.580 6.856 12154 Z= 0.309 Chirality : 0.044 0.141 1300 Planarity : 0.004 0.039 1569 Dihedral : 8.748 87.932 1257 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.37 % Allowed : 18.85 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.25), residues: 1075 helix: 0.22 (0.25), residues: 488 sheet: -0.03 (0.47), residues: 112 loop : -2.52 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 501 HIS 0.004 0.001 HIS B 541 PHE 0.017 0.002 PHE B 438 TYR 0.021 0.002 TYR A 164 ARG 0.009 0.000 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 310) hydrogen bonds : angle 5.17566 ( 900) covalent geometry : bond 0.00305 ( 8989) covalent geometry : angle 0.58000 (12154) *********************** 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 195 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7741 (t0) cc_final: 0.7536 (t0) REVERT: A 595 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5527 (m-80) REVERT: A 673 VAL cc_start: 0.6691 (p) cc_final: 0.6472 (m) REVERT: B 277 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5789 (mm-30) REVERT: B 355 LYS cc_start: 0.8063 (tttp) cc_final: 0.7624 (tttt) REVERT: B 497 MET cc_start: 0.7086 (mmm) cc_final: 0.6789 (mmt) outliers start: 41 outliers final: 18 residues processed: 184 average time/residue: 1.0773 time to fit residues: 212.5928 Evaluate side-chains 168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 390 ASP Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 38 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.193617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.183265 restraints weight = 12033.964| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 1.59 r_work: 0.4335 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2511 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= 0.148 Angle : 0.587 7.419 12154 Z= 0.313 Chirality : 0.045 0.233 1300 Planarity : 0.004 0.033 1569 Dihedral : 8.403 85.977 1255 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.62 % Allowed : 20.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1075 helix: 0.30 (0.25), residues: 482 sheet: -0.17 (0.47), residues: 112 loop : -2.60 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 501 HIS 0.004 0.001 HIS B 216 PHE 0.016 0.002 PHE B 438 TYR 0.017 0.002 TYR A 371 ARG 0.006 0.000 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 310) hydrogen bonds : angle 5.16920 ( 900) covalent geometry : bond 0.00324 ( 8989) covalent geometry : angle 0.58657 (12154) *********************** 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 182 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7767 (t0) cc_final: 0.7553 (t0) REVERT: A 595 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.5402 (m-80) REVERT: A 673 VAL cc_start: 0.6794 (p) cc_final: 0.6553 (m) REVERT: B 153 HIS cc_start: 0.7306 (m90) cc_final: 0.6926 (m90) REVERT: B 277 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5724 (mm-30) REVERT: B 355 LYS cc_start: 0.8109 (tttp) cc_final: 0.7742 (tttt) REVERT: B 497 MET cc_start: 0.7214 (mmm) cc_final: 0.6697 (mmt) outliers start: 34 outliers final: 16 residues processed: 175 average time/residue: 1.0920 time to fit residues: 204.7810 Evaluate side-chains 165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 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 489 MET Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 385 ASN A 492 GLN ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4484 r_free = 0.4484 target = 0.191295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.180931 restraints weight = 12122.097| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 1.58 r_work: 0.4306 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4189 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8989 Z= 0.210 Angle : 0.660 8.836 12154 Z= 0.353 Chirality : 0.048 0.187 1300 Planarity : 0.005 0.050 1569 Dihedral : 8.807 96.311 1255 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.73 % Allowed : 20.98 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1075 helix: 0.11 (0.24), residues: 478 sheet: -0.17 (0.47), residues: 108 loop : -2.74 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 501 HIS 0.007 0.001 HIS B 541 PHE 0.018 0.002 PHE B 224 TYR 0.024 0.002 TYR B 617 ARG 0.011 0.001 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 310) hydrogen bonds : angle 5.37209 ( 900) covalent geometry : bond 0.00472 ( 8989) covalent geometry : angle 0.66024 (12154) *********************** 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 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ARG cc_start: 0.7393 (mpp-170) cc_final: 0.7185 (mtm110) REVERT: A 595 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5636 (m-80) REVERT: A 673 VAL cc_start: 0.6919 (p) cc_final: 0.6708 (m) REVERT: B 153 HIS cc_start: 0.7438 (m90) cc_final: 0.7132 (m90) REVERT: B 241 LYS cc_start: 0.4724 (mmpt) cc_final: 0.4119 (mmpt) REVERT: B 277 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5480 (mm-30) outliers start: 35 outliers final: 19 residues processed: 175 average time/residue: 1.1318 time to fit residues: 212.7777 Evaluate side-chains 168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 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 493 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 663 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 79 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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 = 0.4497 r_free = 0.4497 target = 0.192892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.182971 restraints weight = 12155.184| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.53 r_work: 0.4330 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.4218 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8989 Z= 0.161 Angle : 0.651 12.122 12154 Z= 0.341 Chirality : 0.046 0.174 1300 Planarity : 0.004 0.041 1569 Dihedral : 8.632 103.664 1255 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.30 % Allowed : 21.73 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.25), residues: 1075 helix: 0.09 (0.24), residues: 486 sheet: -0.20 (0.47), residues: 109 loop : -2.55 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 501 HIS 0.005 0.001 HIS B 541 PHE 0.015 0.002 PHE B 482 TYR 0.024 0.002 TYR B 617 ARG 0.008 0.001 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 310) hydrogen bonds : angle 5.32748 ( 900) covalent geometry : bond 0.00353 ( 8989) covalent geometry : angle 0.65144 (12154) *********************** 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 178 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7761 (t0) cc_final: 0.7516 (t0) REVERT: A 595 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5396 (m-80) REVERT: A 673 VAL cc_start: 0.6884 (p) cc_final: 0.6678 (m) REVERT: B 277 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5958 (mm-30) outliers start: 31 outliers final: 19 residues processed: 168 average time/residue: 1.0905 time to fit residues: 196.2587 Evaluate side-chains 165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG 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 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 225 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 476 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 663 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 153 HIS B 213 ASN 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 = 0.4508 r_free = 0.4508 target = 0.193849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.183590 restraints weight = 12170.918| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.57 r_work: 0.4338 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4226 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2814 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= 0.142 Angle : 0.626 9.201 12154 Z= 0.329 Chirality : 0.045 0.177 1300 Planarity : 0.004 0.041 1569 Dihedral : 8.474 108.862 1255 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.13 % Allowed : 23.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.25), residues: 1075 helix: 0.15 (0.24), residues: 488 sheet: -0.30 (0.46), residues: 112 loop : -2.51 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.006 0.001 HIS B 153 PHE 0.015 0.001 PHE B 482 TYR 0.024 0.001 TYR B 617 ARG 0.008 0.000 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 310) hydrogen bonds : angle 5.16718 ( 900) covalent geometry : bond 0.00314 ( 8989) covalent geometry : angle 0.62557 (12154) *********************** 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 166 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7797 (t0) cc_final: 0.7564 (t0) REVERT: A 595 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.5355 (m-80) outliers start: 20 outliers final: 12 residues processed: 163 average time/residue: 1.1238 time to fit residues: 196.0596 Evaluate side-chains 155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 47 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 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 = 0.4505 r_free = 0.4505 target = 0.193438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.183413 restraints weight = 12116.443| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.53 r_work: 0.4342 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4232 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2857 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= 0.157 Angle : 0.659 12.738 12154 Z= 0.342 Chirality : 0.046 0.177 1300 Planarity : 0.004 0.054 1569 Dihedral : 8.460 115.930 1255 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.66 % Allowed : 23.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.25), residues: 1075 helix: 0.18 (0.24), residues: 488 sheet: -0.23 (0.47), residues: 109 loop : -2.50 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 501 HIS 0.008 0.001 HIS B 153 PHE 0.014 0.002 PHE B 438 TYR 0.023 0.002 TYR B 617 ARG 0.015 0.001 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 310) hydrogen bonds : angle 5.24156 ( 900) covalent geometry : bond 0.00351 ( 8989) covalent geometry : angle 0.65948 (12154) ********************** 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: 25 poor density : 145 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASN cc_start: 0.7807 (t0) cc_final: 0.7580 (t0) REVERT: A 595 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.5383 (m-80) REVERT: B 241 LYS cc_start: 0.4092 (mmpt) cc_final: 0.2995 (mmpt) outliers start: 25 outliers final: 18 residues processed: 165 average time/residue: 1.1950 time to fit residues: 210.8327 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 : 0.952 ------------------------------------------------------------------------------- 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 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 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 502 VAL Chi-restraints excluded: chain B residue 505 GLU 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 86 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.4517 r_free = 0.4517 target = 0.194689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.184539 restraints weight = 12140.238| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 1.56 r_work: 0.4353 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8989 Z= 0.137 Angle : 0.631 8.806 12154 Z= 0.332 Chirality : 0.045 0.183 1300 Planarity : 0.004 0.057 1569 Dihedral : 8.377 120.554 1255 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.56 % Allowed : 23.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.25), residues: 1075 helix: 0.18 (0.24), residues: 488 sheet: -0.33 (0.46), residues: 112 loop : -2.45 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 501 HIS 0.007 0.001 HIS B 153 PHE 0.014 0.001 PHE B 438 TYR 0.023 0.002 TYR B 617 ARG 0.014 0.001 ARG B 330 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 310) hydrogen bonds : angle 5.19410 ( 900) covalent geometry : bond 0.00302 ( 8989) covalent geometry : angle 0.63139 (12154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7142.85 seconds wall clock time: 123 minutes 45.58 seconds (7425.58 seconds total)