Starting phenix.real_space_refine on Sat Aug 23 05:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2s_17373/08_2025/8p2s_17373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2s_17373/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p2s_17373/08_2025/8p2s_17373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2s_17373/08_2025/8p2s_17373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p2s_17373/08_2025/8p2s_17373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2s_17373/08_2025/8p2s_17373.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} 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: 2.56, per 1000 atoms: 0.26 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: 0.95 Conformation dependent library (CDL) restraints added in 276.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.18 Time building geometry restraints manager: 1.16 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: 4.520 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9909 Z= 0.123 Angle : 0.546 10.597 13411 Z= 0.293 Chirality : 0.041 0.148 1434 Planarity : 0.003 0.030 1737 Dihedral : 12.819 177.141 3686 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.70 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.000 ARG A 417 TYR 0.020 0.001 TYR B 231 PHE 0.010 0.001 PHE B 224 TRP 0.008 0.001 TRP B 720 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9905) covalent geometry : angle 0.54149 (13405) hydrogen bonds : bond 0.14117 ( 443) hydrogen bonds : angle 6.06829 ( 1269) metal coordination : bond 0.00267 ( 4) metal coordination : angle 3.26291 ( 6) *********************** 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 : 0.242 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: 0.4977 time to fit residues: 157.6661 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 : 0.373 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.146733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.135640 restraints weight = 11947.194| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.37 r_work: 0.3787 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9909 Z= 0.167 Angle : 0.595 11.310 13411 Z= 0.303 Chirality : 0.045 0.196 1434 Planarity : 0.004 0.037 1737 Dihedral : 11.785 175.899 1365 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 2.92 % Allowed : 14.09 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1195 helix: 1.52 (0.22), residues: 574 sheet: -0.18 (0.49), residues: 108 loop : -1.12 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 559 TYR 0.022 0.002 TYR B 231 PHE 0.015 0.002 PHE A 224 TRP 0.010 0.001 TRP A 425 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9905) covalent geometry : angle 0.58321 (13405) hydrogen bonds : bond 0.04164 ( 443) hydrogen bonds : angle 4.60853 ( 1269) metal coordination : bond 0.00498 ( 4) metal coordination : angle 5.69973 ( 6) *********************** 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 260 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7591 (mmm) cc_final: 0.7308 (mmm) REVERT: A 431 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 483 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7293 (mp-120) REVERT: B 161 LYS cc_start: 0.7559 (mtmt) cc_final: 0.7336 (ttpt) REVERT: B 537 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5351 (mt) outliers start: 30 outliers final: 8 residues processed: 245 average time/residue: 0.5313 time to fit residues: 140.0310 Evaluate side-chains 230 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 483 GLN 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 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 492 GLN B 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.145091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.134056 restraints weight = 11949.125| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.36 r_work: 0.3767 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9909 Z= 0.214 Angle : 0.630 10.480 13411 Z= 0.320 Chirality : 0.046 0.164 1434 Planarity : 0.005 0.043 1737 Dihedral : 11.906 177.455 1363 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 3.79 % Allowed : 14.77 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.25), residues: 1195 helix: 1.36 (0.22), residues: 566 sheet: -0.16 (0.49), residues: 108 loop : -1.13 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 148 TYR 0.025 0.002 TYR B 231 PHE 0.017 0.002 PHE A 482 TRP 0.012 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 9905) covalent geometry : angle 0.61855 (13405) hydrogen bonds : bond 0.04450 ( 443) hydrogen bonds : angle 4.67964 ( 1269) metal coordination : bond 0.00534 ( 4) metal coordination : angle 5.57655 ( 6) *********************** 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 265 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 483 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7288 (mp-120) REVERT: B 537 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5197 (mt) outliers start: 39 outliers final: 12 residues processed: 250 average time/residue: 0.5729 time to fit residues: 154.3794 Evaluate side-chains 233 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 483 GLN 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 97 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 597 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.0010 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.0020 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135790 restraints weight = 12108.901| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.38 r_work: 0.3792 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9909 Z= 0.132 Angle : 0.577 10.321 13411 Z= 0.290 Chirality : 0.043 0.144 1434 Planarity : 0.004 0.037 1737 Dihedral : 11.647 176.956 1363 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 3.01 % Allowed : 16.23 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1195 helix: 1.57 (0.22), residues: 567 sheet: 0.02 (0.48), residues: 113 loop : -1.08 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 559 TYR 0.021 0.001 TYR B 231 PHE 0.011 0.001 PHE A 482 TRP 0.008 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9905) covalent geometry : angle 0.56634 (13405) hydrogen bonds : bond 0.03688 ( 443) hydrogen bonds : angle 4.45922 ( 1269) metal coordination : bond 0.00531 ( 4) metal coordination : angle 5.33117 ( 6) *********************** 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 252 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7022 (tm130) REVERT: A 644 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 537 ILE cc_start: 0.5927 (OUTLIER) cc_final: 0.5337 (mt) outliers start: 31 outliers final: 12 residues processed: 240 average time/residue: 0.6068 time to fit residues: 156.8236 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 486 LYS 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 32 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 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 278 GLN A 541 HIS A 548 GLN A 594 GLN A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3985 r_free = 0.3985 target = 0.143981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.132988 restraints weight = 12178.551| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.37 r_work: 0.3765 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9909 Z= 0.192 Angle : 0.619 10.123 13411 Z= 0.313 Chirality : 0.045 0.148 1434 Planarity : 0.004 0.040 1737 Dihedral : 11.836 177.597 1363 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 3.60 % Allowed : 15.74 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.25), residues: 1195 helix: 1.48 (0.22), residues: 567 sheet: -0.06 (0.49), residues: 108 loop : -1.15 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 148 TYR 0.024 0.002 TYR B 231 PHE 0.015 0.002 PHE A 482 TRP 0.010 0.002 TRP A 425 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9905) covalent geometry : angle 0.60884 (13405) hydrogen bonds : bond 0.04194 ( 443) hydrogen bonds : angle 4.56838 ( 1269) metal coordination : bond 0.00502 ( 4) metal coordination : angle 5.43703 ( 6) *********************** 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 260 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7716 (mppt) REVERT: A 431 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 483 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7178 (mp-120) REVERT: A 644 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 668 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7674 (mtt) REVERT: B 451 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5916 (mmm) REVERT: B 537 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5302 (mt) REVERT: B 567 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7104 (mp0) outliers start: 37 outliers final: 12 residues processed: 246 average time/residue: 0.5770 time to fit residues: 152.7829 Evaluate side-chains 235 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 265 LYS 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 483 GLN 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 A residue 668 MET Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 486 LYS 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 567 GLU 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 85 optimal weight: 0.5980 chunk 82 optimal weight: 0.0970 chunk 60 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 360 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 = 0.3998 r_free = 0.3998 target = 0.145550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134390 restraints weight = 12080.694| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.37 r_work: 0.3775 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9909 Z= 0.173 Angle : 0.614 10.007 13411 Z= 0.309 Chirality : 0.045 0.148 1434 Planarity : 0.004 0.040 1737 Dihedral : 11.766 176.787 1362 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 3.01 % Allowed : 17.10 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.25), residues: 1195 helix: 1.46 (0.22), residues: 568 sheet: 0.03 (0.49), residues: 113 loop : -1.17 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 148 TYR 0.023 0.001 TYR B 231 PHE 0.014 0.002 PHE A 482 TRP 0.010 0.002 TRP A 425 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9905) covalent geometry : angle 0.60356 (13405) hydrogen bonds : bond 0.04014 ( 443) hydrogen bonds : angle 4.52556 ( 1269) metal coordination : bond 0.00488 ( 4) metal coordination : angle 5.35144 ( 6) *********************** 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 250 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 483 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7182 (mp-120) REVERT: A 548 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7013 (tm130) REVERT: A 644 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 567 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: B 706 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7360 (tt) outliers start: 31 outliers final: 12 residues processed: 238 average time/residue: 0.5099 time to fit residues: 131.2212 Evaluate side-chains 233 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 476 LYS Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 486 LYS 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 567 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 308 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.144876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133803 restraints weight = 12037.184| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.36 r_work: 0.3765 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9909 Z= 0.207 Angle : 0.644 9.908 13411 Z= 0.325 Chirality : 0.046 0.154 1434 Planarity : 0.004 0.042 1737 Dihedral : 11.847 177.177 1360 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 2.92 % Allowed : 17.49 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.25), residues: 1195 helix: 1.37 (0.22), residues: 562 sheet: -0.14 (0.49), residues: 108 loop : -1.22 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 148 TYR 0.025 0.002 TYR B 231 PHE 0.016 0.002 PHE A 482 TRP 0.011 0.002 TRP A 425 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9905) covalent geometry : angle 0.63418 (13405) hydrogen bonds : bond 0.04314 ( 443) hydrogen bonds : angle 4.61852 ( 1269) metal coordination : bond 0.00485 ( 4) metal coordination : angle 5.42968 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7582 (mt) cc_final: 0.7327 (mt) REVERT: A 292 MET cc_start: 0.8397 (mmp) cc_final: 0.8183 (mmp) REVERT: A 431 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8331 (mm) REVERT: A 453 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7478 (mm) REVERT: A 483 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7212 (mp-120) REVERT: A 644 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 567 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 706 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7361 (tt) outliers start: 30 outliers final: 13 residues processed: 235 average time/residue: 0.5593 time to fit residues: 141.0817 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 : 0.307 ------------------------------------------------------------------------------- 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 483 GLN 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 486 LYS 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 567 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9980 chunk 14 optimal weight: 0.0050 chunk 1 optimal weight: 0.0040 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 541 HIS A 548 GLN A 594 GLN A 611 ASN A 639 HIS ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 442 ASN B 548 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.146412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135257 restraints weight = 12096.111| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.37 r_work: 0.3787 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9909 Z= 0.147 Angle : 0.605 10.296 13411 Z= 0.305 Chirality : 0.044 0.143 1434 Planarity : 0.004 0.040 1737 Dihedral : 11.652 176.428 1360 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 2.62 % Allowed : 18.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1195 helix: 1.48 (0.22), residues: 568 sheet: 0.01 (0.49), residues: 112 loop : -1.17 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 148 TYR 0.021 0.001 TYR B 231 PHE 0.012 0.001 PHE B 129 TRP 0.009 0.001 TRP A 425 HIS 0.005 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9905) covalent geometry : angle 0.59556 (13405) hydrogen bonds : bond 0.03761 ( 443) hydrogen bonds : angle 4.48471 ( 1269) metal coordination : bond 0.00464 ( 4) metal coordination : angle 5.19495 ( 6) *********************** 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 242 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7573 (mt) cc_final: 0.7338 (mt) REVERT: A 431 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 548 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.6928 (tm130) REVERT: A 644 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7349 (mm-30) REVERT: B 546 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6425 (pttt) REVERT: B 567 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: B 687 ASN cc_start: 0.7705 (t0) cc_final: 0.7370 (t0) REVERT: B 706 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7330 (tt) outliers start: 27 outliers final: 12 residues processed: 231 average time/residue: 0.5709 time to fit residues: 141.6262 Evaluate side-chains 228 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 476 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 567 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 69 optimal weight: 0.0870 chunk 80 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 overall best weight: 0.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 HIS A 548 GLN A 611 ASN A 639 HIS ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 289 HIS ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 548 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.149530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138567 restraints weight = 12012.342| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.37 r_work: 0.3828 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9909 Z= 0.108 Angle : 0.569 9.139 13411 Z= 0.287 Chirality : 0.042 0.143 1434 Planarity : 0.004 0.040 1737 Dihedral : 11.370 179.390 1360 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 2.24 % Allowed : 19.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.25), residues: 1195 helix: 1.63 (0.22), residues: 569 sheet: -0.02 (0.49), residues: 112 loop : -1.06 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 148 TYR 0.016 0.001 TYR B 231 PHE 0.010 0.001 PHE A 526 TRP 0.009 0.001 TRP B 409 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9905) covalent geometry : angle 0.55990 (13405) hydrogen bonds : bond 0.03205 ( 443) hydrogen bonds : angle 4.34386 ( 1269) metal coordination : bond 0.00462 ( 4) metal coordination : angle 4.71509 ( 6) *********************** 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 240 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ARG cc_start: 0.6830 (ttm170) cc_final: 0.6591 (ttm170) REVERT: A 350 ILE cc_start: 0.8402 (mp) cc_final: 0.8201 (mp) REVERT: A 431 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 548 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.6721 (tm130) REVERT: A 644 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 151 VAL cc_start: 0.7876 (t) cc_final: 0.7625 (m) REVERT: B 537 ILE cc_start: 0.5701 (OUTLIER) cc_final: 0.5242 (mt) REVERT: B 546 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6451 (ptmt) REVERT: B 567 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: B 662 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6737 (ptp) REVERT: B 687 ASN cc_start: 0.7613 (t0) cc_final: 0.7367 (t0) REVERT: B 706 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7288 (tt) outliers start: 23 outliers final: 6 residues processed: 231 average time/residue: 0.5022 time to fit residues: 125.1104 Evaluate side-chains 220 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 500 LEU 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 567 GLU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.0970 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 483 GLN A 492 GLN A 541 HIS A 548 GLN A 639 HIS ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 242 ASN ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 388 ASN B 395 GLN B 548 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.146451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135201 restraints weight = 12029.388| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.38 r_work: 0.3786 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9909 Z= 0.168 Angle : 0.645 8.766 13411 Z= 0.325 Chirality : 0.045 0.146 1434 Planarity : 0.004 0.041 1737 Dihedral : 11.583 178.984 1360 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 2.24 % Allowed : 19.53 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1195 helix: 1.50 (0.22), residues: 567 sheet: -0.05 (0.50), residues: 112 loop : -1.11 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 148 TYR 0.023 0.001 TYR B 231 PHE 0.012 0.002 PHE A 482 TRP 0.011 0.001 TRP A 353 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9905) covalent geometry : angle 0.63677 (13405) hydrogen bonds : bond 0.03959 ( 443) hydrogen bonds : angle 4.54808 ( 1269) metal coordination : bond 0.00405 ( 4) metal coordination : angle 4.81504 ( 6) ********************** 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 243 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8074 (m-40) cc_final: 0.7763 (m110) REVERT: A 273 ARG cc_start: 0.6999 (ttm170) cc_final: 0.6772 (ttm170) REVERT: A 431 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 548 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.6760 (tm130) REVERT: A 644 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 151 VAL cc_start: 0.7951 (t) cc_final: 0.7743 (m) REVERT: B 299 MET cc_start: 0.8113 (mmt) cc_final: 0.7821 (mmm) REVERT: B 537 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5366 (mt) REVERT: B 546 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6388 (ptmt) REVERT: B 687 ASN cc_start: 0.7677 (t0) cc_final: 0.7364 (t0) REVERT: B 706 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7334 (tt) outliers start: 23 outliers final: 7 residues processed: 235 average time/residue: 0.6000 time to fit residues: 151.8788 Evaluate side-chains 227 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 486 LYS 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 706 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS A 242 ASN A 492 GLN A 541 HIS A 548 GLN A 611 ASN A 639 HIS ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 395 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 = 0.3999 r_free = 0.3999 target = 0.145454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.134263 restraints weight = 11976.674| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.36 r_work: 0.3774 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9909 Z= 0.202 Angle : 0.670 9.022 13411 Z= 0.339 Chirality : 0.046 0.149 1434 Planarity : 0.004 0.040 1737 Dihedral : 11.716 177.672 1360 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 2.04 % Allowed : 20.12 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1195 helix: 1.33 (0.22), residues: 568 sheet: -0.11 (0.49), residues: 112 loop : -1.14 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 148 TYR 0.025 0.002 TYR B 231 PHE 0.016 0.002 PHE A 482 TRP 0.013 0.002 TRP A 353 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9905) covalent geometry : angle 0.66122 (13405) hydrogen bonds : bond 0.04217 ( 443) hydrogen bonds : angle 4.63598 ( 1269) metal coordination : bond 0.00416 ( 4) metal coordination : angle 5.06277 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4268.03 seconds wall clock time: 73 minutes 35.97 seconds (4415.97 seconds total)