Starting phenix.real_space_refine on Fri Feb 14 07:24:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2s_17373/02_2025/8p2s_17373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2s_17373/02_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_17373/02_2025/8p2s_17373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2s_17373/02_2025/8p2s_17373.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2s_17373/02_2025/8p2s_17373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2s_17373/02_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-5592/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: 6.70, per 1000 atoms: 0.69 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: 2.67 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: 1.06 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: 2.96 Time building geometry restraints manager: 3.03 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: 4.200 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.400 Find NCS groups from input model: 0.090 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- 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 9905 Z= 0.167 Angle : 0.541 10.597 13405 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 *********************** 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 : 1.064 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: 1.1864 time to fit residues: 375.5628 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 : 1.202 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.137671 restraints weight = 11963.024| |-----------------------------------------------------------------------------| 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: 0.3694 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- 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 9905 Z= 0.170 Angle : 0.547 6.328 13405 Z= 0.282 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 *********************** 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 : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7570 (mmm) cc_final: 0.7298 (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: 1.2154 time to fit residues: 318.5722 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 : 1.063 ------------------------------------------------------------------------------- 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: 1.9990 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.145537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134430 restraints weight = 12035.868| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.37 r_work: 0.3779 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9905 Z= 0.283 Angle : 0.591 6.675 13405 Z= 0.304 Chirality : 0.045 0.153 1434 Planarity : 0.004 0.039 1737 Dihedral : 11.747 177.111 1363 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.82 % Allowed : 15.26 % Favored : 81.92 % 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: 0.38 (0.25), residues: 1195 helix: 1.48 (0.22), residues: 574 sheet: -0.12 (0.49), residues: 108 loop : -1.09 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.006 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 *********************** 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 : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8360 (mm) REVERT: B 161 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7342 (ttpt) REVERT: B 537 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5367 (mt) outliers start: 29 outliers final: 10 residues processed: 241 average time/residue: 1.2495 time to fit residues: 322.4207 Evaluate side-chains 234 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 1.9990 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 72 optimal weight: 0.0370 chunk 86 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 63 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.147170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136097 restraints weight = 11921.004| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.37 r_work: 0.3801 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9905 Z= 0.185 Angle : 0.549 8.743 13405 Z= 0.280 Chirality : 0.043 0.145 1434 Planarity : 0.004 0.043 1737 Dihedral : 11.564 177.419 1363 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 3.11 % Allowed : 15.84 % Favored : 81.05 % 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: 1.67 (0.22), residues: 568 sheet: 0.03 (0.48), residues: 113 loop : -1.09 (0.28), residues: 514 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 0.011 0.001 PHE A 224 TYR 0.020 0.001 TYR B 231 ARG 0.010 0.000 ARG B 148 *********************** 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: 32 poor density : 221 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 548 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7045 (tm130) REVERT: B 537 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5381 (mt) outliers start: 32 outliers final: 11 residues processed: 239 average time/residue: 1.1704 time to fit residues: 301.2829 Evaluate side-chains 229 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP 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 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: 0.9990 chunk 31 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 57 optimal weight: 0.0970 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.2674 ------------------------------------------------------------------------------- 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 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 308 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.147798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.136724 restraints weight = 11998.019| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.38 r_work: 0.3805 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9905 Z= 0.185 Angle : 0.544 7.869 13405 Z= 0.277 Chirality : 0.042 0.138 1434 Planarity : 0.004 0.035 1737 Dihedral : 11.466 178.366 1361 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 2.53 % Allowed : 17.20 % Favored : 80.27 % 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: 0.64 (0.25), residues: 1195 helix: 1.74 (0.22), residues: 567 sheet: 0.05 (0.49), residues: 113 loop : -1.01 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 425 HIS 0.004 0.001 HIS A 540 PHE 0.010 0.001 PHE B 129 TYR 0.020 0.001 TYR B 231 ARG 0.006 0.000 ARG B 148 *********************** 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 242 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8274 (mm) REVERT: B 537 ILE cc_start: 0.5890 (OUTLIER) cc_final: 0.5392 (mt) outliers start: 26 outliers final: 12 residues processed: 232 average time/residue: 1.1888 time to fit residues: 296.7515 Evaluate side-chains 222 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP 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 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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 388 ASN B 394 ASN B 395 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.144514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133446 restraints weight = 11981.016| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.36 r_work: 0.3759 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9905 Z= 0.365 Angle : 0.643 8.875 13405 Z= 0.328 Chirality : 0.047 0.148 1434 Planarity : 0.005 0.039 1737 Dihedral : 11.896 177.931 1361 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 3.50 % Allowed : 16.81 % Favored : 79.69 % 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: 0.26 (0.25), residues: 1195 helix: 1.35 (0.22), residues: 568 sheet: -0.07 (0.50), residues: 108 loop : -1.12 (0.28), residues: 519 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 A 482 TYR 0.026 0.002 TYR B 231 ARG 0.006 0.001 ARG B 417 *********************** 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 264 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 THR cc_start: 0.8167 (m) cc_final: 0.7507 (p) REVERT: A 431 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 548 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7024 (tm130) REVERT: A 644 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7263 (mm-30) outliers start: 36 outliers final: 14 residues processed: 249 average time/residue: 1.1344 time to fit residues: 304.6594 Evaluate side-chains 233 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 369 ASP 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 618 LYS 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 597 VAL 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: 0.9980 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 360 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133466 restraints weight = 12086.514| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.36 r_work: 0.3760 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9905 Z= 0.360 Angle : 0.657 10.884 13405 Z= 0.335 Chirality : 0.047 0.153 1434 Planarity : 0.004 0.043 1737 Dihedral : 11.882 176.605 1361 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 3.21 % Allowed : 17.40 % Favored : 79.40 % 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: 0.11 (0.25), residues: 1195 helix: 1.27 (0.22), residues: 562 sheet: -0.08 (0.50), residues: 108 loop : -1.23 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 PHE 0.021 0.002 PHE B 129 TYR 0.026 0.002 TYR B 231 ARG 0.004 0.001 ARG A 233 *********************** 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 248 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8353 (mm) REVERT: A 453 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7460 (mm) REVERT: A 644 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 668 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7593 (mtt) REVERT: B 127 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7007 (mmt) REVERT: B 706 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7370 (tt) outliers start: 33 outliers final: 14 residues processed: 233 average time/residue: 1.1672 time to fit residues: 292.7418 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 : 1.008 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 369 ASP 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 A residue 668 MET 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 706 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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 360 ASN B 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133312 restraints weight = 12216.659| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.38 r_work: 0.3762 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9905 Z= 0.333 Angle : 0.653 12.107 13405 Z= 0.333 Chirality : 0.047 0.187 1434 Planarity : 0.004 0.044 1737 Dihedral : 11.853 176.546 1360 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 2.72 % Allowed : 17.88 % Favored : 79.40 % 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: 0.10 (0.25), residues: 1195 helix: 1.29 (0.22), residues: 562 sheet: -0.12 (0.49), residues: 108 loop : -1.25 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 PHE 0.019 0.002 PHE B 129 TYR 0.025 0.002 TYR B 231 ARG 0.004 0.001 ARG A 233 *********************** 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 244 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8143 (m-40) cc_final: 0.7908 (m110) REVERT: A 431 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 453 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7463 (mm) REVERT: A 548 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.6928 (tm130) REVERT: A 644 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 546 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6441 (pttt) REVERT: B 706 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7354 (tt) outliers start: 28 outliers final: 13 residues processed: 228 average time/residue: 1.1969 time to fit residues: 293.2285 Evaluate side-chains 230 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 369 ASP 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 548 GLN 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 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS 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: 0.9990 chunk 100 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 492 GLN 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 360 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.144173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133023 restraints weight = 12112.329| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.37 r_work: 0.3757 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9905 Z= 0.366 Angle : 0.667 7.723 13405 Z= 0.343 Chirality : 0.047 0.161 1434 Planarity : 0.005 0.044 1737 Dihedral : 11.904 176.823 1360 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 2.53 % Allowed : 18.08 % Favored : 79.40 % 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: 0.06 (0.25), residues: 1195 helix: 1.22 (0.22), residues: 560 sheet: -0.05 (0.48), residues: 113 loop : -1.26 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 PHE 0.022 0.002 PHE B 129 TYR 0.026 0.002 TYR B 231 ARG 0.004 0.001 ARG A 233 *********************** 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 238 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 453 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7440 (mm) REVERT: A 548 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6839 (tm130) REVERT: A 644 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 493 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: B 546 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6474 (pttt) outliers start: 26 outliers final: 13 residues processed: 224 average time/residue: 1.1993 time to fit residues: 288.6972 Evaluate side-chains 229 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 369 ASP 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 548 GLN 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 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 68 optimal weight: 0.0040 chunk 17 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.4170 ------------------------------------------------------------------------------- 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 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 360 ASN B 442 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 = 0.4006 r_free = 0.4006 target = 0.145984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134774 restraints weight = 12230.611| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.38 r_work: 0.3782 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9905 Z= 0.250 Angle : 0.633 11.082 13405 Z= 0.323 Chirality : 0.045 0.147 1434 Planarity : 0.004 0.042 1737 Dihedral : 11.738 176.561 1360 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 1.94 % Allowed : 18.76 % Favored : 79.30 % 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: 0.20 (0.25), residues: 1195 helix: 1.34 (0.22), residues: 567 sheet: 0.01 (0.49), residues: 112 loop : -1.22 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.005 0.001 HIS A 540 PHE 0.016 0.002 PHE B 129 TYR 0.022 0.001 TYR B 231 ARG 0.003 0.000 ARG B 559 ********************** 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 236 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.8296 (mtp) cc_final: 0.7916 (mtp) REVERT: A 360 ASN cc_start: 0.7926 (p0) cc_final: 0.7706 (p0) REVERT: A 431 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8320 (mm) REVERT: A 644 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 546 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6467 (pttt) outliers start: 20 outliers final: 11 residues processed: 227 average time/residue: 1.2047 time to fit residues: 294.0364 Evaluate side-chains 221 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP 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 537 ILE Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 310 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 395 GLN B 548 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134404 restraints weight = 12046.487| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.36 r_work: 0.3774 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9905 Z= 0.301 Angle : 0.645 8.054 13405 Z= 0.332 Chirality : 0.046 0.150 1434 Planarity : 0.004 0.042 1737 Dihedral : 11.804 177.608 1360 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 1.94 % Allowed : 19.14 % 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: 0.15 (0.25), residues: 1195 helix: 1.28 (0.22), residues: 568 sheet: -0.07 (0.49), residues: 113 loop : -1.22 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.006 0.001 HIS A 540 PHE 0.019 0.002 PHE B 129 TYR 0.024 0.002 TYR B 231 ARG 0.004 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8362.76 seconds wall clock time: 148 minutes 25.80 seconds (8905.80 seconds total)