Starting phenix.real_space_refine on Mon Jun 9 09:23:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1e_28796/06_2025/8f1e_28796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1e_28796/06_2025/8f1e_28796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f1e_28796/06_2025/8f1e_28796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1e_28796/06_2025/8f1e_28796.map" model { file = "/net/cci-nas-00/data/ceres_data/8f1e_28796/06_2025/8f1e_28796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1e_28796/06_2025/8f1e_28796.cif" } resolution = 3.28 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 163 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 39 5.16 5 C 6509 2.51 5 N 1681 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10174 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7442 Classifications: {'peptide': 934} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 907} Chain breaks: 1 Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 629 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "C" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 677 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1393 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.70, per 1000 atoms: 0.76 Number of scatterers: 10174 At special positions: 0 Unit cell: (97.94, 109.56, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 3 15.00 Mg 1 11.99 O 1941 8.00 N 1681 7.00 C 6509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 2 sheets defined 75.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.525A pdb=" N GLY A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 11 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 31 removed outlier: 3.783A pdb=" N SER A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.835A pdb=" N VAL A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.535A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.751A pdb=" N THR A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.567A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 204 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 236 removed outlier: 3.649A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 270 through 296 removed outlier: 4.119A pdb=" N MET A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASN A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 321 removed outlier: 3.965A pdb=" N LEU A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.529A pdb=" N ASN A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.963A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 384 through 402 removed outlier: 4.275A pdb=" N LEU A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.572A pdb=" N GLU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 removed outlier: 3.732A pdb=" N LEU A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.604A pdb=" N PHE A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.973A pdb=" N GLY A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.573A pdb=" N LEU A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 613 through 634 Proline residue: A 623 - end of helix removed outlier: 3.592A pdb=" N VAL A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 656 removed outlier: 3.673A pdb=" N VAL A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.749A pdb=" N ASN A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 684 through 701 removed outlier: 3.661A pdb=" N GLU A 693 " --> pdb=" O GLN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.579A pdb=" N LYS A 716 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 717 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 732 removed outlier: 4.628A pdb=" N MET A 732 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 745 removed outlier: 4.180A pdb=" N LEU A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 767 removed outlier: 4.398A pdb=" N GLY A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 787 Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 804 through 818 removed outlier: 3.894A pdb=" N LEU A 808 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 840 Processing helix chain 'A' and resid 841 through 847 removed outlier: 3.945A pdb=" N GLN A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 Processing helix chain 'A' and resid 965 through 980 removed outlier: 3.649A pdb=" N LYS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 991 Processing helix chain 'A' and resid 992 through 1003 removed outlier: 3.503A pdb=" N ALA A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.780A pdb=" N GLY B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 removed outlier: 4.693A pdb=" N VAL B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'C' and resid 41 through 52 Processing helix chain 'C' and resid 58 through 88 removed outlier: 3.843A pdb=" N MET C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 105 removed outlier: 3.528A pdb=" N ILE C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 126 removed outlier: 3.710A pdb=" N LYS C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 77 through 82 removed outlier: 3.896A pdb=" N TYR D 82 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 114 removed outlier: 4.158A pdb=" N TYR D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.810A pdb=" N ARG D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 138 through 143' Processing helix chain 'D' and resid 160 through 172 Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.760A pdb=" N ARG B 43 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 54 removed outlier: 3.654A pdb=" N ILE D 61 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE D 13 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TRP D 66 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU D 15 " --> pdb=" O TRP D 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR D 68 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU D 17 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE D 119 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TYR D 149 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D 121 " --> pdb=" O TYR D 149 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1947 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: 3.16 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3294 1.34 - 1.46: 2199 1.46 - 1.58: 4792 1.58 - 1.70: 5 1.70 - 1.82: 58 Bond restraints: 10348 Sorted by residual: bond pdb=" N ILE C 104 " pdb=" CA ILE C 104 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.77e+00 bond pdb=" N VAL B 55 " pdb=" CA VAL B 55 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 bond pdb=" N VAL C 69 " pdb=" CA VAL C 69 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.46e+00 bond pdb=" N VAL A 831 " pdb=" CA VAL A 831 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.05e+00 bond pdb=" N VAL C 101 " pdb=" CA VAL C 101 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.19e-02 7.06e+03 6.75e+00 ... (remaining 10343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13751 2.25 - 4.49: 225 4.49 - 6.74: 30 6.74 - 8.99: 9 8.99 - 11.24: 7 Bond angle restraints: 14022 Sorted by residual: angle pdb=" N LYS B 75 " pdb=" CA LYS B 75 " pdb=" C LYS B 75 " ideal model delta sigma weight residual 113.23 108.37 4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" N ASN B 74 " pdb=" CA ASN B 74 " pdb=" C ASN B 74 " ideal model delta sigma weight residual 113.01 108.44 4.57 1.20e+00 6.94e-01 1.45e+01 angle pdb=" N ASN C 66 " pdb=" CA ASN C 66 " pdb=" C ASN C 66 " ideal model delta sigma weight residual 111.11 106.56 4.55 1.20e+00 6.94e-01 1.44e+01 angle pdb=" PB GTP D 202 " pdb=" O3B GTP D 202 " pdb=" PG GTP D 202 " ideal model delta sigma weight residual 120.50 131.74 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CB MET A 866 " pdb=" CG MET A 866 " pdb=" SD MET A 866 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 ... (remaining 14017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 5849 27.46 - 54.91: 421 54.91 - 82.37: 28 82.37 - 109.83: 7 109.83 - 137.28: 3 Dihedral angle restraints: 6308 sinusoidal: 2537 harmonic: 3771 Sorted by residual: dihedral pdb=" C8 GTP D 202 " pdb=" C1' GTP D 202 " pdb=" N9 GTP D 202 " pdb=" O4' GTP D 202 " ideal model delta sinusoidal sigma weight residual 104.59 -32.69 137.28 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" O3A GTP D 202 " pdb=" O3B GTP D 202 " pdb=" PB GTP D 202 " pdb=" PG GTP D 202 " ideal model delta sinusoidal sigma weight residual 303.79 174.97 128.82 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O2G GTP D 202 " pdb=" O3B GTP D 202 " pdb=" PG GTP D 202 " pdb=" PB GTP D 202 " ideal model delta sinusoidal sigma weight residual 177.30 -61.76 -120.94 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1266 0.043 - 0.087: 294 0.087 - 0.130: 87 0.130 - 0.174: 10 0.174 - 0.217: 3 Chirality restraints: 1660 Sorted by residual: chirality pdb=" C3' GTP D 202 " pdb=" C2' GTP D 202 " pdb=" C4' GTP D 202 " pdb=" O3' GTP D 202 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR C 122 " pdb=" CA THR C 122 " pdb=" OG1 THR C 122 " pdb=" CG2 THR C 122 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 1657 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 75 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C ARG C 75 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG C 75 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 76 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 123 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 124 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 80 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO B 81 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " -0.021 5.00e-02 4.00e+02 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 66 2.46 - 3.07: 7252 3.07 - 3.68: 16230 3.68 - 4.29: 22869 4.29 - 4.90: 36372 Nonbonded interactions: 82789 Sorted by model distance: nonbonded pdb="MG MG D 201 " pdb=" O3B GTP D 202 " model vdw 1.853 2.170 nonbonded pdb="MG MG D 201 " pdb=" O2A GTP D 202 " model vdw 2.011 2.170 nonbonded pdb=" OG1 THR D 44 " pdb="MG MG D 201 " model vdw 2.162 2.170 nonbonded pdb=" O GLU A 975 " pdb=" OG SER A 978 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR A 254 " pdb=" OD2 ASP A 284 " model vdw 2.294 3.040 ... (remaining 82784 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.660 Find NCS groups from input model: 0.120 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.047 10348 Z= 0.215 Angle : 0.668 11.237 14022 Z= 0.387 Chirality : 0.042 0.217 1660 Planarity : 0.003 0.039 1769 Dihedral : 17.516 137.281 3846 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.17 % Allowed : 30.37 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1263 helix: 1.74 (0.17), residues: 872 sheet: 1.64 (0.85), residues: 37 loop : -0.24 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.002 0.000 HIS B 83 PHE 0.010 0.001 PHE A 578 TYR 0.023 0.001 TYR A 513 ARG 0.008 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.21156 ( 654) hydrogen bonds : angle 6.05543 ( 1947) covalent geometry : bond 0.00329 (10348) covalent geometry : angle 0.66784 (14022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8929 (pt0) cc_final: 0.8508 (pt0) REVERT: C 62 MET cc_start: 0.7388 (pmm) cc_final: 0.7116 (pmm) REVERT: C 65 LEU cc_start: 0.9086 (mm) cc_final: 0.8819 (tp) REVERT: C 71 ASP cc_start: 0.9307 (t0) cc_final: 0.9033 (m-30) REVERT: C 96 GLU cc_start: 0.8986 (mp0) cc_final: 0.8572 (mp0) REVERT: D 55 TYR cc_start: 0.8771 (m-80) cc_final: 0.8428 (m-80) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.2700 time to fit residues: 27.4653 Evaluate side-chains 50 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 530 GLN A 627 ASN A 829 ASN A 835 ASN B 74 ASN B 95 ASN C 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.072855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.049576 restraints weight = 39816.138| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.38 r_work: 0.2819 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10348 Z= 0.139 Angle : 0.564 11.111 14022 Z= 0.291 Chirality : 0.040 0.158 1660 Planarity : 0.004 0.041 1769 Dihedral : 6.831 126.056 1374 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.61 % Allowed : 28.46 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1263 helix: 1.82 (0.17), residues: 901 sheet: 1.63 (1.02), residues: 30 loop : -0.10 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 66 HIS 0.005 0.001 HIS B 83 PHE 0.038 0.001 PHE A 887 TYR 0.014 0.001 TYR B 51 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 654) hydrogen bonds : angle 4.26052 ( 1947) covalent geometry : bond 0.00308 (10348) covalent geometry : angle 0.56363 (14022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9355 (mmm) cc_final: 0.9021 (mmt) REVERT: B 57 GLU cc_start: 0.9104 (pt0) cc_final: 0.8669 (pt0) REVERT: B 65 GLU cc_start: 0.9360 (tt0) cc_final: 0.9151 (tm-30) REVERT: C 62 MET cc_start: 0.7432 (pmm) cc_final: 0.7074 (pmm) REVERT: C 96 GLU cc_start: 0.8981 (mp0) cc_final: 0.8600 (mp0) REVERT: C 102 ARG cc_start: 0.8380 (mmm160) cc_final: 0.8093 (mmm160) REVERT: D 55 TYR cc_start: 0.8954 (m-80) cc_final: 0.8578 (m-80) REVERT: D 175 GLN cc_start: 0.8886 (mp10) cc_final: 0.8604 (pm20) outliers start: 30 outliers final: 18 residues processed: 87 average time/residue: 0.2343 time to fit residues: 29.7205 Evaluate side-chains 66 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN C 98 GLN D 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.068791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044655 restraints weight = 39924.333| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.35 r_work: 0.2810 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10348 Z= 0.112 Angle : 0.512 10.808 14022 Z= 0.261 Chirality : 0.038 0.132 1660 Planarity : 0.003 0.040 1769 Dihedral : 5.884 117.312 1372 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.35 % Allowed : 28.02 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.06 (0.23), residues: 1263 helix: 1.93 (0.17), residues: 894 sheet: 1.53 (0.88), residues: 37 loop : -0.14 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 66 HIS 0.003 0.001 HIS A 207 PHE 0.029 0.001 PHE A 887 TYR 0.014 0.001 TYR B 51 ARG 0.007 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 654) hydrogen bonds : angle 3.95592 ( 1947) covalent geometry : bond 0.00248 (10348) covalent geometry : angle 0.51169 (14022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9280 (mmm) cc_final: 0.8982 (mmt) REVERT: A 866 MET cc_start: 0.8394 (pmm) cc_final: 0.8179 (pmm) REVERT: B 57 GLU cc_start: 0.9119 (pt0) cc_final: 0.8654 (pt0) REVERT: B 65 GLU cc_start: 0.9391 (tt0) cc_final: 0.9158 (tm-30) REVERT: C 96 GLU cc_start: 0.9082 (mp0) cc_final: 0.8642 (mp0) REVERT: D 55 TYR cc_start: 0.8843 (m-80) cc_final: 0.8467 (m-80) REVERT: D 175 GLN cc_start: 0.8849 (mp10) cc_final: 0.8523 (pm20) outliers start: 27 outliers final: 17 residues processed: 80 average time/residue: 0.1992 time to fit residues: 24.3122 Evaluate side-chains 62 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.067894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043602 restraints weight = 39286.829| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.29 r_work: 0.2780 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10348 Z= 0.148 Angle : 0.542 10.726 14022 Z= 0.271 Chirality : 0.039 0.157 1660 Planarity : 0.003 0.039 1769 Dihedral : 5.692 117.782 1372 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.39 % Allowed : 27.42 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.08 (0.24), residues: 1263 helix: 1.94 (0.17), residues: 892 sheet: 1.37 (0.89), residues: 37 loop : -0.10 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 66 HIS 0.003 0.001 HIS A 207 PHE 0.021 0.001 PHE A 887 TYR 0.014 0.001 TYR B 51 ARG 0.006 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 654) hydrogen bonds : angle 3.91100 ( 1947) covalent geometry : bond 0.00343 (10348) covalent geometry : angle 0.54222 (14022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 50 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9284 (mmm) cc_final: 0.8989 (mmt) REVERT: B 57 GLU cc_start: 0.9159 (pt0) cc_final: 0.8689 (pt0) REVERT: C 59 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8195 (tp-100) REVERT: C 62 MET cc_start: 0.7590 (pmm) cc_final: 0.6783 (ppp) REVERT: C 96 GLU cc_start: 0.9064 (mp0) cc_final: 0.8600 (mp0) REVERT: D 55 TYR cc_start: 0.8856 (m-80) cc_final: 0.8464 (m-80) REVERT: D 86 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8801 (mt0) REVERT: D 164 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9214 (tp) REVERT: D 175 GLN cc_start: 0.8853 (mp10) cc_final: 0.8525 (pm20) outliers start: 39 outliers final: 21 residues processed: 85 average time/residue: 0.2223 time to fit residues: 29.1787 Evaluate side-chains 68 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 775 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.070820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047032 restraints weight = 39298.248| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.45 r_work: 0.2790 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10348 Z= 0.169 Angle : 0.548 11.594 14022 Z= 0.278 Chirality : 0.040 0.154 1660 Planarity : 0.003 0.040 1769 Dihedral : 5.686 121.116 1372 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.57 % Allowed : 26.81 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.10 (0.24), residues: 1263 helix: 1.95 (0.17), residues: 890 sheet: 0.61 (0.94), residues: 38 loop : 0.04 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.001 PHE A 887 TYR 0.014 0.001 TYR B 51 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 654) hydrogen bonds : angle 3.93265 ( 1947) covalent geometry : bond 0.00396 (10348) covalent geometry : angle 0.54772 (14022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 50 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9377 (mmm) cc_final: 0.9055 (mmt) REVERT: B 57 GLU cc_start: 0.9187 (pt0) cc_final: 0.8721 (pt0) REVERT: C 59 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8124 (tp-100) REVERT: C 62 MET cc_start: 0.7309 (pmm) cc_final: 0.6394 (ppp) REVERT: C 96 GLU cc_start: 0.9050 (mp0) cc_final: 0.8586 (mp0) REVERT: D 55 TYR cc_start: 0.9033 (m-80) cc_final: 0.8625 (m-80) REVERT: D 86 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8719 (mt0) REVERT: D 175 GLN cc_start: 0.9039 (mp10) cc_final: 0.8766 (pm20) outliers start: 41 outliers final: 27 residues processed: 87 average time/residue: 0.1887 time to fit residues: 25.6120 Evaluate side-chains 72 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN A 894 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.068395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.044000 restraints weight = 39385.641| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.33 r_work: 0.2784 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10348 Z= 0.107 Angle : 0.525 12.010 14022 Z= 0.260 Chirality : 0.039 0.151 1660 Planarity : 0.003 0.044 1769 Dihedral : 5.534 117.967 1372 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.35 % Allowed : 28.11 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.06 (0.24), residues: 1263 helix: 1.95 (0.17), residues: 892 sheet: 0.66 (0.94), residues: 38 loop : -0.08 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 66 HIS 0.003 0.000 HIS A 207 PHE 0.019 0.001 PHE A 887 TYR 0.014 0.001 TYR B 51 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 654) hydrogen bonds : angle 3.83054 ( 1947) covalent geometry : bond 0.00240 (10348) covalent geometry : angle 0.52491 (14022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9322 (mmm) cc_final: 0.9031 (mmt) REVERT: D 55 TYR cc_start: 0.8893 (m-80) cc_final: 0.8468 (m-80) REVERT: D 86 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: D 137 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8923 (p) REVERT: D 175 GLN cc_start: 0.8971 (mp10) cc_final: 0.8712 (pm20) outliers start: 27 outliers final: 17 residues processed: 71 average time/residue: 0.2275 time to fit residues: 27.9144 Evaluate side-chains 59 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 76 optimal weight: 0.0770 chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.068725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044287 restraints weight = 39391.089| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.36 r_work: 0.2797 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10348 Z= 0.101 Angle : 0.512 11.777 14022 Z= 0.257 Chirality : 0.039 0.165 1660 Planarity : 0.003 0.041 1769 Dihedral : 5.402 115.034 1372 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.61 % Allowed : 27.94 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.10 (0.24), residues: 1263 helix: 1.99 (0.17), residues: 894 sheet: 0.66 (0.94), residues: 38 loop : -0.14 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 66 HIS 0.002 0.000 HIS B 83 PHE 0.016 0.001 PHE A 887 TYR 0.011 0.001 TYR B 51 ARG 0.006 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 654) hydrogen bonds : angle 3.74979 ( 1947) covalent geometry : bond 0.00222 (10348) covalent geometry : angle 0.51172 (14022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8431 (t-90) REVERT: A 173 MET cc_start: 0.9264 (mmm) cc_final: 0.9007 (mmt) REVERT: C 114 VAL cc_start: 0.9311 (m) cc_final: 0.9098 (p) REVERT: D 55 TYR cc_start: 0.8804 (m-80) cc_final: 0.8404 (m-80) REVERT: D 137 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8960 (p) outliers start: 30 outliers final: 21 residues processed: 72 average time/residue: 0.2193 time to fit residues: 25.3806 Evaluate side-chains 66 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain D residue 32 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 152 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 116 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.068404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.043494 restraints weight = 40203.400| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.45 r_work: 0.2770 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10348 Z= 0.109 Angle : 0.520 11.266 14022 Z= 0.260 Chirality : 0.039 0.159 1660 Planarity : 0.003 0.041 1769 Dihedral : 5.340 114.472 1372 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.61 % Allowed : 27.68 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.18 (0.24), residues: 1263 helix: 2.04 (0.17), residues: 897 sheet: 1.10 (0.88), residues: 42 loop : -0.13 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 66 HIS 0.002 0.000 HIS B 83 PHE 0.014 0.001 PHE A 887 TYR 0.010 0.001 TYR B 51 ARG 0.005 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 654) hydrogen bonds : angle 3.73025 ( 1947) covalent geometry : bond 0.00250 (10348) covalent geometry : angle 0.51969 (14022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8483 (t-90) REVERT: A 173 MET cc_start: 0.9287 (mmm) cc_final: 0.9002 (mmt) REVERT: A 781 CYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9004 (p) REVERT: C 114 VAL cc_start: 0.9311 (m) cc_final: 0.9084 (p) REVERT: D 55 TYR cc_start: 0.8808 (m-80) cc_final: 0.8415 (m-80) REVERT: D 86 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8743 (mt0) REVERT: D 137 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8971 (p) REVERT: D 175 GLN cc_start: 0.8994 (mp10) cc_final: 0.8714 (pm20) outliers start: 30 outliers final: 20 residues processed: 73 average time/residue: 0.1957 time to fit residues: 22.3121 Evaluate side-chains 65 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.068630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043839 restraints weight = 39757.190| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.42 r_work: 0.2771 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10348 Z= 0.109 Angle : 0.533 11.565 14022 Z= 0.268 Chirality : 0.039 0.162 1660 Planarity : 0.003 0.041 1769 Dihedral : 5.331 114.092 1372 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.70 % Allowed : 27.42 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.20 (0.24), residues: 1263 helix: 2.05 (0.17), residues: 897 sheet: 1.11 (0.88), residues: 42 loop : -0.12 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 66 HIS 0.002 0.000 HIS B 83 PHE 0.014 0.001 PHE A 887 TYR 0.009 0.001 TYR A 511 ARG 0.011 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 654) hydrogen bonds : angle 3.73646 ( 1947) covalent geometry : bond 0.00251 (10348) covalent geometry : angle 0.53313 (14022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8528 (t-90) REVERT: A 173 MET cc_start: 0.9301 (mmm) cc_final: 0.9017 (mmt) REVERT: A 712 MET cc_start: 0.8220 (tmm) cc_final: 0.8016 (tmm) REVERT: A 781 CYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8999 (p) REVERT: D 86 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8730 (mt0) REVERT: D 137 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8959 (p) outliers start: 31 outliers final: 22 residues processed: 74 average time/residue: 0.2044 time to fit residues: 23.5599 Evaluate side-chains 68 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain D residue 32 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.068541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.043358 restraints weight = 40750.331| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.52 r_work: 0.2769 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10348 Z= 0.110 Angle : 0.535 12.421 14022 Z= 0.268 Chirality : 0.039 0.154 1660 Planarity : 0.003 0.043 1769 Dihedral : 5.298 113.507 1372 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.44 % Allowed : 27.59 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.24 (0.24), residues: 1263 helix: 2.08 (0.17), residues: 897 sheet: 1.12 (0.88), residues: 42 loop : -0.10 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 28 HIS 0.002 0.000 HIS B 83 PHE 0.013 0.001 PHE A 887 TYR 0.009 0.001 TYR B 51 ARG 0.011 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 654) hydrogen bonds : angle 3.72429 ( 1947) covalent geometry : bond 0.00252 (10348) covalent geometry : angle 0.53531 (14022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8558 (t-90) REVERT: A 173 MET cc_start: 0.9312 (mmm) cc_final: 0.9026 (mmt) REVERT: A 705 ARG cc_start: 0.9221 (mtm-85) cc_final: 0.9016 (mtm-85) REVERT: A 781 CYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9006 (p) REVERT: C 62 MET cc_start: 0.7373 (pmm) cc_final: 0.6928 (ppp) REVERT: C 88 LYS cc_start: 0.9070 (pptt) cc_final: 0.8860 (pptt) REVERT: C 96 GLU cc_start: 0.9073 (mp0) cc_final: 0.8547 (mp0) REVERT: D 86 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8692 (mt0) REVERT: D 137 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8951 (p) outliers start: 28 outliers final: 23 residues processed: 73 average time/residue: 0.2119 time to fit residues: 23.4289 Evaluate side-chains 72 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain D residue 32 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 79 optimal weight: 0.0040 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.0040 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN A 775 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.068922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043965 restraints weight = 40115.662| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.49 r_work: 0.2801 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10348 Z= 0.101 Angle : 0.548 12.414 14022 Z= 0.270 Chirality : 0.039 0.155 1660 Planarity : 0.003 0.041 1769 Dihedral : 5.217 110.727 1372 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.35 % Allowed : 27.94 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2.25 (0.24), residues: 1263 helix: 2.09 (0.17), residues: 897 sheet: 1.75 (0.90), residues: 36 loop : -0.18 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 66 HIS 0.002 0.000 HIS B 83 PHE 0.014 0.001 PHE A 887 TYR 0.014 0.001 TYR D 148 ARG 0.010 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 654) hydrogen bonds : angle 3.69110 ( 1947) covalent geometry : bond 0.00224 (10348) covalent geometry : angle 0.54777 (14022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5624.96 seconds wall clock time: 99 minutes 38.22 seconds (5978.22 seconds total)