Starting phenix.real_space_refine on Sat Nov 16 00:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/11_2024/8p2s_17373.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/11_2024/8p2s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/11_2024/8p2s_17373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/11_2024/8p2s_17373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/11_2024/8p2s_17373.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2s_17373/11_2024/8p2s_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-5513/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: 6.66, 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: 2.71 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: 0.93 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: 3.04 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 2.710 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.310 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- 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 : 1.017 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: 1.2344 time to fit residues: 391.0388 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 : 1.171 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 LYS cc_start: 0.7273 (mtmt) cc_final: 0.7057 (mtmt) outliers start: 26 outliers final: 7 residues processed: 244 average time/residue: 1.2109 time to fit residues: 317.0941 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 : 1.099 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 37 optimal weight: 0.0980 chunk 87 optimal weight: 0.0670 overall best weight: 0.3118 ------------------------------------------------------------------------------- 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 B 308 ASN B 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9905 Z= 0.195 Angle : 0.545 6.356 13405 Z= 0.280 Chirality : 0.043 0.165 1434 Planarity : 0.004 0.036 1737 Dihedral : 11.476 177.033 1363 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 2.53 % Allowed : 15.45 % Favored : 82.02 % 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: 0.57 (0.25), residues: 1195 helix: 1.67 (0.22), residues: 574 sheet: -0.07 (0.49), residues: 108 loop : -1.04 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 PHE 0.012 0.001 PHE A 224 TYR 0.020 0.001 TYR B 231 ARG 0.008 0.000 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 243 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 537 ILE cc_start: 0.5237 (OUTLIER) cc_final: 0.4886 (mt) outliers start: 26 outliers final: 10 residues processed: 233 average time/residue: 1.2222 time to fit residues: 306.0641 Evaluate side-chains 221 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR 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 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 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.0060 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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 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 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9905 Z= 0.243 Angle : 0.572 8.664 13405 Z= 0.292 Chirality : 0.044 0.137 1434 Planarity : 0.004 0.037 1737 Dihedral : 11.604 177.465 1363 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 3.01 % Allowed : 16.03 % Favored : 80.95 % 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: 1.63 (0.22), residues: 568 sheet: -0.04 (0.50), residues: 108 loop : -1.11 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 425 HIS 0.006 0.001 HIS A 540 PHE 0.014 0.002 PHE A 482 TYR 0.023 0.001 TYR B 231 ARG 0.006 0.000 ARG B 559 *********************** 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 : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8245 (mm) REVERT: A 548 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.6917 (tm130) REVERT: B 537 ILE cc_start: 0.5264 (OUTLIER) cc_final: 0.4884 (mt) outliers start: 31 outliers final: 10 residues processed: 239 average time/residue: 1.1993 time to fit residues: 308.2393 Evaluate side-chains 232 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 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 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 1 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 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 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 394 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9905 Z= 0.293 Angle : 0.599 8.449 13405 Z= 0.307 Chirality : 0.045 0.146 1434 Planarity : 0.004 0.038 1737 Dihedral : 11.737 177.777 1363 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 2.92 % Allowed : 16.91 % Favored : 80.17 % 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: 0.41 (0.25), residues: 1195 helix: 1.52 (0.22), residues: 568 sheet: 0.07 (0.49), residues: 113 loop : -1.12 (0.28), residues: 514 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 0.005 0.001 ARG B 559 *********************** 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 250 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7327 (mt) cc_final: 0.7083 (mt) REVERT: A 431 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 548 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7053 (tm130) REVERT: B 161 LYS cc_start: 0.7450 (ttpt) cc_final: 0.7238 (ttpt) outliers start: 30 outliers final: 12 residues processed: 239 average time/residue: 1.2160 time to fit residues: 313.5438 Evaluate side-chains 231 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 583 LEU 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 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 39 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 360 ASN B 395 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9905 Z= 0.281 Angle : 0.606 8.309 13405 Z= 0.310 Chirality : 0.045 0.149 1434 Planarity : 0.004 0.039 1737 Dihedral : 11.745 177.064 1363 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 3.21 % Allowed : 16.81 % Favored : 79.98 % 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: 1.49 (0.22), residues: 568 sheet: -0.02 (0.48), residues: 113 loop : -1.12 (0.28), residues: 514 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 0.015 0.002 PHE A 482 TYR 0.023 0.002 TYR B 231 ARG 0.004 0.000 ARG B 559 *********************** 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 258 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7323 (mt) cc_final: 0.7091 (mt) REVERT: A 431 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8255 (mm) outliers start: 33 outliers final: 13 residues processed: 241 average time/residue: 1.1460 time to fit residues: 297.7345 Evaluate side-chains 232 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 583 LEU 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 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 111 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9905 Z= 0.284 Angle : 0.618 9.779 13405 Z= 0.315 Chirality : 0.045 0.149 1434 Planarity : 0.004 0.039 1737 Dihedral : 11.741 176.892 1362 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 2.82 % Allowed : 17.40 % Favored : 79.79 % 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: 0.32 (0.25), residues: 1195 helix: 1.50 (0.22), residues: 566 sheet: -0.18 (0.49), residues: 108 loop : -1.17 (0.28), residues: 521 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 0.017 0.002 PHE B 129 TYR 0.023 0.002 TYR B 231 ARG 0.004 0.000 ARG B 559 *********************** 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 249 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7334 (mt) cc_final: 0.7079 (mt) REVERT: A 326 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7815 (mtp85) REVERT: A 431 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 548 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6801 (tm130) REVERT: B 127 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6148 (mmt) outliers start: 29 outliers final: 12 residues processed: 238 average time/residue: 1.1428 time to fit residues: 293.1304 Evaluate side-chains 228 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 548 GLN Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 127 MET 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 Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.4980 chunk 46 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 0.0040 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.2592 ------------------------------------------------------------------------------- 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 ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 360 ASN B 395 GLN B 442 ASN B 548 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9905 Z= 0.194 Angle : 0.588 9.778 13405 Z= 0.298 Chirality : 0.043 0.164 1434 Planarity : 0.004 0.038 1737 Dihedral : 11.523 177.402 1360 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 2.24 % Allowed : 18.66 % Favored : 79.11 % 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: 0.45 (0.25), residues: 1195 helix: 1.63 (0.22), residues: 566 sheet: -0.21 (0.49), residues: 108 loop : -1.09 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.004 0.001 HIS A 540 PHE 0.012 0.001 PHE B 312 TYR 0.019 0.001 TYR B 231 ARG 0.004 0.000 ARG B 559 *********************** 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 241 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7256 (mt) cc_final: 0.7023 (mt) REVERT: A 213 ASN cc_start: 0.7929 (m-40) cc_final: 0.7711 (m110) REVERT: A 326 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7778 (mtp85) REVERT: A 431 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8200 (mm) REVERT: B 163 TYR cc_start: 0.7761 (m-80) cc_final: 0.7558 (m-80) outliers start: 23 outliers final: 7 residues processed: 231 average time/residue: 1.1914 time to fit residues: 295.6354 Evaluate side-chains 220 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 212 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 46 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN 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 360 ASN B 388 ASN B 395 GLN B 540 HIS B 548 GLN ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9905 Z= 0.270 Angle : 0.627 8.999 13405 Z= 0.321 Chirality : 0.045 0.180 1434 Planarity : 0.004 0.038 1737 Dihedral : 11.563 175.436 1356 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 1.75 % Allowed : 19.63 % Favored : 78.62 % 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: 1.49 (0.22), residues: 568 sheet: -0.13 (0.48), residues: 113 loop : -1.09 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 425 HIS 0.006 0.001 HIS B 540 PHE 0.017 0.002 PHE B 129 TYR 0.023 0.001 TYR B 231 ARG 0.003 0.000 ARG B 559 *********************** 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 231 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7119 (mtm) REVERT: A 431 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 548 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.6741 (tm130) REVERT: B 299 MET cc_start: 0.7738 (mmt) cc_final: 0.7459 (mmm) outliers start: 18 outliers final: 9 residues processed: 224 average time/residue: 1.2168 time to fit residues: 293.3827 Evaluate side-chains 222 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 215 MET 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 B residue 97 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN 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 242 ASN B 360 ASN B 395 GLN B 548 GLN ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2542 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= 0.324 Angle : 0.657 9.701 13405 Z= 0.337 Chirality : 0.046 0.149 1434 Planarity : 0.004 0.039 1737 Dihedral : 11.638 175.679 1356 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 1.65 % Allowed : 19.53 % 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: 0.26 (0.25), residues: 1195 helix: 1.39 (0.22), residues: 566 sheet: -0.15 (0.48), residues: 113 loop : -1.13 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.007 0.001 HIS A 540 PHE 0.020 0.002 PHE B 129 TYR 0.024 0.002 TYR B 231 ARG 0.004 0.001 ARG A 233 ********************** 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 232 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 548 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.6631 (tm130) REVERT: B 299 MET cc_start: 0.7751 (mmt) cc_final: 0.7477 (mmm) outliers start: 17 outliers final: 9 residues processed: 221 average time/residue: 1.2182 time to fit residues: 289.2900 Evaluate side-chains 226 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 B residue 242 ASN Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 602 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.0980 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 360 ASN 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 242 ASN B 360 ASN B 395 GLN B 548 GLN B 675 HIS ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134584 restraints weight = 11974.106| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.33 r_work: 0.3786 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9905 Z= 0.278 Angle : 0.643 8.891 13405 Z= 0.331 Chirality : 0.045 0.149 1434 Planarity : 0.004 0.038 1737 Dihedral : 11.619 175.059 1356 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 1.65 % Allowed : 19.53 % 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: 0.25 (0.25), residues: 1195 helix: 1.37 (0.22), residues: 568 sheet: -0.15 (0.49), residues: 113 loop : -1.14 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.006 0.001 HIS A 540 PHE 0.018 0.002 PHE B 129 TYR 0.022 0.001 TYR B 231 ARG 0.003 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5088.27 seconds wall clock time: 91 minutes 43.52 seconds (5503.52 seconds total)