Starting phenix.real_space_refine on Wed Apr 30 21:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2s_17373/04_2025/8p2s_17373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2s_17373/04_2025/8p2s_17373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p2s_17373/04_2025/8p2s_17373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2s_17373/04_2025/8p2s_17373.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2s_17373/04_2025/8p2s_17373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2s_17373/04_2025/8p2s_17373.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 9 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 6082 2.51 5 N 1687 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4417 Classifications: {'peptide': 550} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 529} Chain breaks: 1 Chain: "B" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5184 Classifications: {'peptide': 651} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 629} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' MG': 1, ' ZN': 1, 'GTP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9173 SG CYS B 680 14.461 51.845 61.872 1.00 63.96 S ATOM 9195 SG CYS B 683 13.936 55.137 59.924 1.00 64.44 S ATOM 9286 SG CYS B 695 12.496 54.640 63.508 1.00 71.47 S ATOM 9308 SG CYS B 698 11.067 52.943 60.445 1.00 72.94 S Time building chain proxies: 7.36, per 1000 atoms: 0.76 Number of scatterers: 9694 At special positions: 0 Unit cell: (77.456, 105.472, 115.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 60 16.00 P 9 15.00 Mg 2 11.99 O 1853 8.00 N 1687 7.00 C 6082 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: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 698 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 695 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 680 " Number of angles added : 6 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 51.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 121 through 139 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 175 through 183 removed outlier: 4.095A pdb=" N ILE A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 229 through 248 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.646A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 302 Processing helix chain 'A' and resid 322 through 339 Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.671A pdb=" N GLN A 395 " --> pdb=" O THR A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 455 through 486 Processing helix chain 'A' and resid 487 through 488 No H-bonds generated for 'chain 'A' and resid 487 through 488' Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.546A pdb=" N LEU A 507 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.336A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 544 through 570 Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.889A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 635 Proline residue: A 630 - end of helix removed outlier: 4.234A pdb=" N ASP A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'B' and resid 86 through 105 removed outlier: 3.596A pdb=" N VAL B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 141 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 175 through 183 removed outlier: 4.094A pdb=" N ILE B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 Processing helix chain 'B' and resid 223 through 248 Proline residue: B 230 - end of helix removed outlier: 3.599A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 272 through 302 removed outlier: 3.739A pdb=" N ASN B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.655A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.858A pdb=" N GLN B 395 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.797A pdb=" N CYS B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 487 removed outlier: 4.094A pdb=" N THR B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.512A pdb=" N PHE B 493 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 513 through 518 removed outlier: 4.369A pdb=" N ASN B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 570 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.811A pdb=" N LYS B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 635 Proline residue: B 630 - end of helix removed outlier: 4.258A pdb=" N ASP B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 4.000A pdb=" N HIS B 651 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN B 652 " --> pdb=" O ASP B 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 647 through 652' Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.526A pdb=" N GLU B 657 " --> pdb=" O PRO B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 720 removed outlier: 3.579A pdb=" N TRP B 720 " --> pdb=" O THR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158 removed outlier: 4.843A pdb=" N ASN A 435 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY A 523 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER A 437 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY A 525 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ILE A 527 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE A 441 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.604A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN A 219 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN A 316 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 221 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE A 641 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASN A 674 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 643 " --> pdb=" O ASN A 674 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.660A pdb=" N GLY B 523 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B 438 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY B 525 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR B 440 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE B 527 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASN B 442 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 522 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 576 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE B 524 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 173 removed outlier: 6.230A pdb=" N VAL B 172 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN B 219 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN B 316 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 221 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER B 313 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE B 352 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 315 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 354 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 317 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE B 641 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN B 674 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 643 " --> pdb=" O ASN B 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AA7, first strand: chain 'B' and resid 686 through 687 removed outlier: 3.807A pdb=" N GLN B 707 " --> pdb=" O VAL B 714 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1269 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: 2.73 Time building geometry restraints manager: 3.21 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: 3230 1.34 - 1.46: 2040 1.46 - 1.58: 4522 1.58 - 1.69: 15 1.69 - 1.81: 98 Bond restraints: 9905 Sorted by residual: bond pdb=" CA ILE B 453 " pdb=" CB ILE B 453 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 7.51e-01 bond pdb=" CA GLY B 538 " pdb=" C GLY B 538 " ideal model delta sigma weight residual 1.514 1.526 -0.012 1.41e-02 5.03e+03 6.85e-01 bond pdb=" N GLY A 523 " pdb=" CA GLY A 523 " ideal model delta sigma weight residual 1.452 1.442 0.010 1.40e-02 5.10e+03 5.17e-01 bond pdb=" C VAL B 516 " pdb=" O VAL B 516 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.19e-02 7.06e+03 5.02e-01 bond pdb=" CG1 ILE A 197 " pdb=" CD1 ILE A 197 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.88e-01 ... (remaining 9900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 13269 2.12 - 4.24: 115 4.24 - 6.36: 19 6.36 - 8.48: 1 8.48 - 10.60: 1 Bond angle restraints: 13405 Sorted by residual: angle pdb=" C ASN A 308 " pdb=" N GLN A 309 " pdb=" CA GLN A 309 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" CA LEU B 536 " pdb=" CB LEU B 536 " pdb=" CG LEU B 536 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.17e+00 angle pdb=" CA VAL B 516 " pdb=" C VAL B 516 " pdb=" N ILE B 517 " ideal model delta sigma weight residual 116.60 120.23 -3.63 1.45e+00 4.76e-01 6.28e+00 angle pdb=" N TYR A 407 " pdb=" CA TYR A 407 " pdb=" C TYR A 407 " ideal model delta sigma weight residual 110.19 107.15 3.04 1.24e+00 6.50e-01 6.00e+00 angle pdb=" CA VAL A 516 " pdb=" C VAL A 516 " pdb=" N ILE A 517 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.33e+00 ... (remaining 13400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 5845 35.43 - 70.86: 71 70.86 - 106.29: 8 106.29 - 141.71: 2 141.71 - 177.14: 2 Dihedral angle restraints: 5928 sinusoidal: 2432 harmonic: 3496 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 124.54 177.14 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 802 " pdb=" C1' TTP B 802 " pdb=" N1 TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sinusoidal sigma weight residual 301.68 125.82 175.87 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' TTP A 801 " pdb=" O5' TTP A 801 " pdb=" PA TTP A 801 " pdb=" O3A TTP A 801 " ideal model delta sinusoidal sigma weight residual 179.97 42.01 137.96 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 5925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 835 0.030 - 0.059: 381 0.059 - 0.089: 141 0.089 - 0.119: 66 0.119 - 0.148: 11 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CG LEU B 536 " pdb=" CB LEU B 536 " pdb=" CD1 LEU B 536 " pdb=" CD2 LEU B 536 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.49e-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 4.71e-01 chirality pdb=" CA ILE B 703 " pdb=" N ILE B 703 " pdb=" C ILE B 703 " pdb=" CB ILE B 703 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1431 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 295 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C PHE B 295 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE B 295 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 296 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 277 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C GLU B 277 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU B 277 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN B 278 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 231 " 0.014 2.00e-02 2.50e+03 8.84e-03 1.56e+00 pdb=" CG TYR B 231 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 231 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 231 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 231 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 231 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 231 " 0.003 2.00e-02 2.50e+03 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 165 2.68 - 3.23: 9698 3.23 - 3.79: 16295 3.79 - 4.34: 23002 4.34 - 4.90: 36997 Nonbonded interactions: 86157 Sorted by model distance: nonbonded pdb=" O3G TTP A 801 " pdb="MG MG B 801 " model vdw 2.120 2.170 nonbonded pdb=" OE1 GLN A 290 " pdb="MG MG A 802 " model vdw 2.172 2.170 nonbonded pdb=" OD1 ASN B 674 " pdb=" NH1 ARG B 708 " model vdw 2.232 3.120 nonbonded pdb=" OD1 ASN B 652 " pdb=" OG SER B 654 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP A 468 " pdb=" NH1 ARG A 561 " model vdw 2.236 3.120 ... (remaining 86152 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.470 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 : 0.003 0.027 9909 Z= 0.123 Angle : 0.546 10.597 13411 Z= 0.293 Chirality : 0.041 0.148 1434 Planarity : 0.003 0.030 1737 Dihedral : 12.819 177.141 3686 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 3.01 % Allowed : 5.83 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1195 helix: 1.41 (0.22), residues: 563 sheet: 0.24 (0.51), residues: 109 loop : -1.20 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 720 HIS 0.004 0.001 HIS A 540 PHE 0.010 0.001 PHE B 224 TYR 0.020 0.001 TYR B 231 ARG 0.003 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.14117 ( 443) hydrogen bonds : angle 6.06829 ( 1269) metal coordination : bond 0.00267 ( 4) metal coordination : angle 3.26291 ( 6) covalent geometry : bond 0.00254 ( 9905) covalent geometry : angle 0.54149 (13405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 292 MET cc_start: 0.8366 (mmp) cc_final: 0.7631 (mmp) REVERT: B 546 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5868 (pptt) outliers start: 31 outliers final: 4 residues processed: 295 average time/residue: 1.1665 time to fit residues: 370.3526 Evaluate side-chains 231 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 226 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.2980 chunk 90 optimal weight: 0.0170 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 0.0570 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 455 ASN A 492 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 219 GLN B 242 ASN B 290 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 388 ASN B 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.137671 restraints weight = 11963.014| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.37 r_work: 0.3819 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9909 Z= 0.120 Angle : 0.559 11.248 13411 Z= 0.283 Chirality : 0.043 0.186 1434 Planarity : 0.004 0.034 1737 Dihedral : 11.567 176.592 1365 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 2.53 % Allowed : 13.80 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1195 helix: 1.66 (0.22), residues: 576 sheet: -0.13 (0.49), residues: 108 loop : -1.06 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 720 HIS 0.004 0.001 HIS A 540 PHE 0.012 0.001 PHE B 224 TYR 0.019 0.001 TYR B 231 ARG 0.007 0.000 ARG B 559 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 443) hydrogen bonds : angle 4.47637 ( 1269) metal coordination : bond 0.00513 ( 4) metal coordination : angle 5.53094 ( 6) covalent geometry : bond 0.00259 ( 9905) covalent geometry : angle 0.54692 (13405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7572 (mmm) cc_final: 0.7300 (mmm) REVERT: B 161 LYS cc_start: 0.7477 (mtmt) cc_final: 0.7276 (mtmt) outliers start: 26 outliers final: 7 residues processed: 244 average time/residue: 1.1884 time to fit residues: 312.7121 Evaluate side-chains 223 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN A 360 ASN A 388 ASN A 483 GLN A 492 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134449 restraints weight = 12044.053| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.37 r_work: 0.3778 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9909 Z= 0.190 Angle : 0.605 10.275 13411 Z= 0.307 Chirality : 0.045 0.145 1434 Planarity : 0.004 0.039 1737 Dihedral : 11.752 177.103 1363 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.82 % Allowed : 15.35 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1195 helix: 1.47 (0.22), residues: 574 sheet: -0.12 (0.49), residues: 108 loop : -1.10 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 PHE 0.016 0.002 PHE A 482 TYR 0.024 0.002 TYR B 231 ARG 0.008 0.001 ARG B 559 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 443) hydrogen bonds : angle 4.57249 ( 1269) metal coordination : bond 0.00513 ( 4) metal coordination : angle 5.33768 ( 6) covalent geometry : bond 0.00446 ( 9905) covalent geometry : angle 0.59422 (13405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8360 (mm) REVERT: B 537 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5391 (mt) outliers start: 29 outliers final: 10 residues processed: 241 average time/residue: 1.3784 time to fit residues: 356.9073 Evaluate side-chains 230 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 63 optimal weight: 0.0770 chunk 58 optimal weight: 0.9980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 388 ASN A 492 GLN A 541 HIS A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 219 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 548 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135660 restraints weight = 11919.583| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.37 r_work: 0.3792 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9909 Z= 0.141 Angle : 0.573 10.154 13411 Z= 0.288 Chirality : 0.043 0.143 1434 Planarity : 0.004 0.043 1737 Dihedral : 11.634 176.972 1363 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 3.01 % Allowed : 16.13 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1195 helix: 1.61 (0.22), residues: 568 sheet: 0.01 (0.49), residues: 113 loop : -1.10 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 PHE 0.012 0.002 PHE A 482 TYR 0.021 0.001 TYR B 231 ARG 0.009 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 443) hydrogen bonds : angle 4.46230 ( 1269) metal coordination : bond 0.00508 ( 4) metal coordination : angle 5.21454 ( 6) covalent geometry : bond 0.00321 ( 9905) covalent geometry : angle 0.56203 (13405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 548 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7056 (tm130) REVERT: B 537 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5403 (mt) outliers start: 31 outliers final: 12 residues processed: 240 average time/residue: 1.3312 time to fit residues: 344.6377 Evaluate side-chains 233 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 0.0070 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 388 ASN A 541 HIS A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS B 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135876 restraints weight = 11980.854| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.37 r_work: 0.3794 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9909 Z= 0.143 Angle : 0.572 10.016 13411 Z= 0.288 Chirality : 0.043 0.144 1434 Planarity : 0.004 0.036 1737 Dihedral : 11.598 177.392 1363 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 2.82 % Allowed : 16.72 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1195 helix: 1.64 (0.22), residues: 567 sheet: 0.08 (0.49), residues: 113 loop : -1.06 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.007 0.001 HIS B 540 PHE 0.012 0.002 PHE A 482 TYR 0.022 0.001 TYR B 231 ARG 0.007 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 443) hydrogen bonds : angle 4.45589 ( 1269) metal coordination : bond 0.00491 ( 4) metal coordination : angle 5.17383 ( 6) covalent geometry : bond 0.00328 ( 9905) covalent geometry : angle 0.56134 (13405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 644 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 662 MET cc_start: 0.7448 (ptp) cc_final: 0.7179 (ptm) outliers start: 29 outliers final: 12 residues processed: 233 average time/residue: 1.2043 time to fit residues: 303.2871 Evaluate side-chains 224 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 74 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 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 388 ASN A 492 GLN A 541 HIS A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.144679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133627 restraints weight = 11968.045| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.36 r_work: 0.3762 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9909 Z= 0.226 Angle : 0.650 10.092 13411 Z= 0.327 Chirality : 0.047 0.149 1434 Planarity : 0.005 0.040 1737 Dihedral : 11.940 177.891 1363 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 3.21 % Allowed : 17.20 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1195 helix: 1.42 (0.22), residues: 560 sheet: -0.05 (0.50), residues: 108 loop : -1.20 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 PHE 0.019 0.002 PHE A 482 TYR 0.026 0.002 TYR B 231 ARG 0.005 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 443) hydrogen bonds : angle 4.64640 ( 1269) metal coordination : bond 0.00491 ( 4) metal coordination : angle 5.50016 ( 6) covalent geometry : bond 0.00533 ( 9905) covalent geometry : angle 0.64006 (13405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8354 (mm) REVERT: A 548 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7012 (tm130) REVERT: A 644 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 662 MET cc_start: 0.7549 (ptp) cc_final: 0.7256 (ptm) outliers start: 33 outliers final: 15 residues processed: 248 average time/residue: 1.1121 time to fit residues: 298.5291 Evaluate side-chains 233 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 388 ASN A 492 GLN A 541 HIS A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.144468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133373 restraints weight = 12080.343| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.36 r_work: 0.3760 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9909 Z= 0.217 Angle : 0.657 10.273 13411 Z= 0.330 Chirality : 0.046 0.147 1434 Planarity : 0.004 0.042 1737 Dihedral : 11.880 176.812 1363 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 3.01 % Allowed : 18.08 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1195 helix: 1.30 (0.22), residues: 562 sheet: -0.06 (0.50), residues: 108 loop : -1.24 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 PHE 0.020 0.002 PHE B 129 TYR 0.025 0.002 TYR B 231 ARG 0.004 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 443) hydrogen bonds : angle 4.66273 ( 1269) metal coordination : bond 0.00501 ( 4) metal coordination : angle 5.60254 ( 6) covalent geometry : bond 0.00515 ( 9905) covalent geometry : angle 0.64644 (13405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 453 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7432 (mm) REVERT: A 644 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 127 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6986 (mmt) REVERT: B 493 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 706 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7365 (tt) outliers start: 31 outliers final: 14 residues processed: 233 average time/residue: 1.3758 time to fit residues: 345.3121 Evaluate side-chains 234 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 57 optimal weight: 0.0370 chunk 58 optimal weight: 0.4980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 388 ASN A 492 GLN A 541 HIS A 548 GLN A 594 GLN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 219 GLN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 442 ASN B 548 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.135766 restraints weight = 12246.682| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.39 r_work: 0.3792 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9909 Z= 0.137 Angle : 0.598 9.947 13411 Z= 0.300 Chirality : 0.043 0.145 1434 Planarity : 0.004 0.039 1737 Dihedral : 11.607 177.353 1362 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 2.72 % Allowed : 18.46 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1195 helix: 1.51 (0.22), residues: 568 sheet: 0.07 (0.49), residues: 112 loop : -1.13 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 PHE 0.013 0.001 PHE B 129 TYR 0.020 0.001 TYR B 231 ARG 0.004 0.000 ARG B 559 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 443) hydrogen bonds : angle 4.48107 ( 1269) metal coordination : bond 0.00480 ( 4) metal coordination : angle 5.22662 ( 6) covalent geometry : bond 0.00315 ( 9905) covalent geometry : angle 0.58772 (13405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8285 (mm) REVERT: A 548 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.6909 (tm130) REVERT: A 644 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7252 (mm-30) REVERT: B 334 GLN cc_start: 0.7796 (mt0) cc_final: 0.7588 (mt0) REVERT: B 546 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6448 (pttt) REVERT: B 687 ASN cc_start: 0.7718 (t0) cc_final: 0.7365 (t0) REVERT: B 706 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7326 (tt) outliers start: 28 outliers final: 10 residues processed: 226 average time/residue: 1.1646 time to fit residues: 283.4970 Evaluate side-chains 219 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 0.4980 chunk 100 optimal weight: 0.2980 chunk 113 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 541 HIS A 548 GLN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 388 ASN B 395 GLN B 540 HIS B 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134943 restraints weight = 12086.266| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.37 r_work: 0.3781 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9909 Z= 0.170 Angle : 0.629 9.634 13411 Z= 0.317 Chirality : 0.045 0.147 1434 Planarity : 0.004 0.039 1737 Dihedral : 11.685 177.090 1362 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 1.94 % Allowed : 19.53 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1195 helix: 1.41 (0.22), residues: 567 sheet: -0.02 (0.49), residues: 113 loop : -1.15 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 425 HIS 0.007 0.001 HIS B 540 PHE 0.014 0.002 PHE B 129 TYR 0.023 0.001 TYR B 231 ARG 0.003 0.000 ARG B 559 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 443) hydrogen bonds : angle 4.56661 ( 1269) metal coordination : bond 0.00448 ( 4) metal coordination : angle 5.17258 ( 6) covalent geometry : bond 0.00400 ( 9905) covalent geometry : angle 0.61905 (13405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8090 (m-40) cc_final: 0.7793 (m110) REVERT: A 431 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8300 (mm) REVERT: A 548 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.6859 (tm130) REVERT: A 644 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 239 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6691 (mm-30) REVERT: B 283 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7784 (mtmp) REVERT: B 546 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6435 (ptmt) REVERT: B 706 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7328 (tt) outliers start: 20 outliers final: 8 residues processed: 230 average time/residue: 1.1414 time to fit residues: 282.4017 Evaluate side-chains 224 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 548 GLN A 594 GLN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133610 restraints weight = 12191.528| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.38 r_work: 0.3763 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9909 Z= 0.221 Angle : 0.679 9.964 13411 Z= 0.342 Chirality : 0.047 0.166 1434 Planarity : 0.004 0.041 1737 Dihedral : 11.833 177.386 1360 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 1.46 % Allowed : 20.41 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1195 helix: 1.26 (0.22), residues: 560 sheet: -0.14 (0.50), residues: 107 loop : -1.24 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.007 0.001 HIS A 540 PHE 0.018 0.002 PHE A 482 TYR 0.025 0.002 TYR B 231 ARG 0.004 0.001 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 443) hydrogen bonds : angle 4.70293 ( 1269) metal coordination : bond 0.00457 ( 4) metal coordination : angle 5.43671 ( 6) covalent geometry : bond 0.00525 ( 9905) covalent geometry : angle 0.66965 (13405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8203 (m-40) cc_final: 0.7983 (m110) REVERT: A 431 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 548 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.6818 (tm130) REVERT: A 644 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 546 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6445 (ptmt) REVERT: B 706 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7343 (tt) outliers start: 15 outliers final: 8 residues processed: 233 average time/residue: 1.3516 time to fit residues: 338.4737 Evaluate side-chains 232 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 0.2980 chunk 94 optimal weight: 0.3980 chunk 111 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 492 GLN A 548 GLN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 548 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.145975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134973 restraints weight = 12054.814| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.37 r_work: 0.3782 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9909 Z= 0.169 Angle : 0.643 9.845 13411 Z= 0.325 Chirality : 0.045 0.151 1434 Planarity : 0.004 0.040 1737 Dihedral : 11.720 176.377 1360 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 1.55 % Allowed : 20.02 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1195 helix: 1.27 (0.22), residues: 568 sheet: -0.12 (0.49), residues: 113 loop : -1.15 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.006 0.001 HIS A 540 PHE 0.014 0.002 PHE A 482 TYR 0.022 0.001 TYR B 231 ARG 0.005 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 443) hydrogen bonds : angle 4.62346 ( 1269) metal coordination : bond 0.00455 ( 4) metal coordination : angle 5.30576 ( 6) covalent geometry : bond 0.00397 ( 9905) covalent geometry : angle 0.63328 (13405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9438.68 seconds wall clock time: 164 minutes 58.31 seconds (9898.31 seconds total)