Starting phenix.real_space_refine on Thu Nov 14 18:28:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/11_2024/8iww_35781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/11_2024/8iww_35781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/11_2024/8iww_35781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/11_2024/8iww_35781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/11_2024/8iww_35781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iww_35781/11_2024/8iww_35781.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 Al 1 5.89 5 P 2 5.49 5 S 52 5.16 5 C 4355 2.51 5 N 1145 2.21 5 O 1288 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6848 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6815 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 35, 'TRANS': 854} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.66, per 1000 atoms: 0.68 Number of scatterers: 6848 At special positions: 0 Unit cell: (115.92, 100.8, 107.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 S 52 16.00 P 2 15.00 Al 1 13.00 F 4 9.00 O 1288 8.00 N 1145 7.00 C 4355 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: 1.53 Conformation dependent library (CDL) restraints added in 870.3 milliseconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 52.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 100 through 130 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 256 through 286 Processing helix chain 'A' and resid 290 through 306 removed outlier: 3.724A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.981A pdb=" N GLU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.514A pdb=" N ILE A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.719A pdb=" N LEU A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.763A pdb=" N LEU A 442 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 444 " --> pdb=" O GLY A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 444' Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 503 through 520 removed outlier: 3.744A pdb=" N ALA A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 removed outlier: 3.508A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.554A pdb=" N ALA A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.881A pdb=" N ILE A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.745A pdb=" N MET A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.668A pdb=" N ALA A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 721 removed outlier: 4.056A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.566A pdb=" N ARG A 760 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 798 removed outlier: 3.914A pdb=" N LEU A 798 " --> pdb=" O PHE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 826 removed outlier: 3.576A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 860 Processing helix chain 'A' and resid 861 through 866 removed outlier: 3.663A pdb=" N LYS A 866 " --> pdb=" O PRO A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 909 removed outlier: 4.061A pdb=" N SER A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 909 " --> pdb=" O ILE A 905 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151 removed outlier: 5.268A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS A 162 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 183 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 195 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151 removed outlier: 5.268A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS A 162 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.143A pdb=" N VAL A 346 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 657 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.169A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 462 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU A 451 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS A 464 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.422A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE A 538 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TYR A 493 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N GLY A 540 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 12.844A pdb=" N SER A 495 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 18.667A pdb=" N VAL A 542 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 417 Processing sheet with id=AA7, first strand: chain 'A' and resid 592 through 594 removed outlier: 8.174A pdb=" N GLN A 592 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE A 617 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 594 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 660 through 661 removed outlier: 6.560A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 392 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.73 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: 2204 1.34 - 1.46: 804 1.46 - 1.57: 3858 1.57 - 1.69: 3 1.69 - 1.81: 88 Bond restraints: 6957 Sorted by residual: bond pdb=" F3 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.684 1.787 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" F2 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.685 1.777 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" F4 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.686 1.766 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.454 0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 6952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.19: 9420 13.19 - 26.37: 4 26.37 - 39.56: 0 39.56 - 52.75: 0 52.75 - 65.93: 2 Bond angle restraints: 9426 Sorted by residual: angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F2 ALF A1002 " ideal model delta sigma weight residual 108.68 174.61 -65.93 3.00e+00 1.11e-01 4.83e+02 angle pdb=" F3 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 109.63 175.41 -65.78 3.00e+00 1.11e-01 4.81e+02 angle pdb=" F2 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 110.21 83.92 26.29 3.00e+00 1.11e-01 7.68e+01 angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 109.02 90.70 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F3 ALF A1002 " ideal model delta sigma weight residual 109.69 91.45 18.24 3.00e+00 1.11e-01 3.70e+01 ... (remaining 9421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 3949 21.92 - 43.84: 254 43.84 - 65.77: 25 65.77 - 87.69: 12 87.69 - 109.61: 1 Dihedral angle restraints: 4241 sinusoidal: 1679 harmonic: 2562 Sorted by residual: dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 -169.61 109.61 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" CA SER A 840 " pdb=" C SER A 840 " pdb=" N ASN A 841 " pdb=" CA ASN A 841 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A 374 " pdb=" CG GLU A 374 " pdb=" CD GLU A 374 " pdb=" OE1 GLU A 374 " ideal model delta sinusoidal sigma weight residual 0.00 85.10 -85.10 1 3.00e+01 1.11e-03 9.76e+00 ... (remaining 4238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 942 0.052 - 0.104: 166 0.104 - 0.156: 22 0.156 - 0.208: 0 0.208 - 0.260: 1 Chirality restraints: 1131 Sorted by residual: chirality pdb=" C2' ADP A1001 " pdb=" C1' ADP A1001 " pdb=" C3' ADP A1001 " pdb=" O2' ADP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASP A 180 " pdb=" N ASP A 180 " pdb=" C ASP A 180 " pdb=" CB ASP A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA LEU A 134 " pdb=" N LEU A 134 " pdb=" C LEU A 134 " pdb=" CB LEU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1128 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1001 " 0.033 2.00e-02 2.50e+03 1.50e-02 6.17e+00 pdb=" C2 ADP A1001 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ADP A1001 " -0.011 2.00e-02 2.50e+03 pdb=" C5 ADP A1001 " -0.006 2.00e-02 2.50e+03 pdb=" C6 ADP A1001 " 0.019 2.00e-02 2.50e+03 pdb=" C8 ADP A1001 " -0.001 2.00e-02 2.50e+03 pdb=" N1 ADP A1001 " 0.005 2.00e-02 2.50e+03 pdb=" N3 ADP A1001 " -0.016 2.00e-02 2.50e+03 pdb=" N6 ADP A1001 " 0.011 2.00e-02 2.50e+03 pdb=" N7 ADP A1001 " -0.017 2.00e-02 2.50e+03 pdb=" N9 ADP A1001 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 743 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 744 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 135 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 136 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.018 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1593 2.79 - 3.31: 6725 3.31 - 3.84: 11316 3.84 - 4.37: 12548 4.37 - 4.90: 21520 Nonbonded interactions: 53702 Sorted by model distance: nonbonded pdb=" O ARG A 417 " pdb=" OG1 THR A 420 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP A 172 " pdb=" OG SER A 239 " model vdw 2.259 3.040 nonbonded pdb=" O ILE A 306 " pdb="CA CA A1000 " model vdw 2.303 2.510 nonbonded pdb=" OG SER A 186 " pdb=" O GLU A 191 " model vdw 2.329 3.040 nonbonded pdb=" O ARG A 468 " pdb=" NE2 GLN A 471 " model vdw 2.342 3.120 ... (remaining 53697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 0.107 6957 Z= 0.202 Angle : 1.221 65.934 9426 Z= 0.496 Chirality : 0.039 0.260 1131 Planarity : 0.004 0.044 1186 Dihedral : 14.519 109.609 2583 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.13 % Allowed : 2.75 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.69 (0.26), residues: 886 helix: -0.27 (0.23), residues: 438 sheet: -1.86 (0.46), residues: 118 loop : -1.88 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 460 HIS 0.001 0.000 HIS A 624 PHE 0.009 0.001 PHE A 176 TYR 0.005 0.001 TYR A 493 ARG 0.002 0.000 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3927 (mmm) cc_final: 0.3188 (mmp) REVERT: A 81 ASN cc_start: 0.6219 (t0) cc_final: 0.5666 (m-40) REVERT: A 110 ILE cc_start: 0.8752 (tt) cc_final: 0.8477 (tt) REVERT: A 172 ASP cc_start: 0.7591 (m-30) cc_final: 0.7287 (m-30) REVERT: A 355 LEU cc_start: 0.8674 (tp) cc_final: 0.7621 (tp) REVERT: A 452 TYR cc_start: 0.6880 (m-80) cc_final: 0.6307 (m-80) REVERT: A 510 TYR cc_start: 0.8759 (m-10) cc_final: 0.8448 (m-80) REVERT: A 725 PHE cc_start: 0.3823 (m-80) cc_final: 0.3001 (m-80) REVERT: A 834 PHE cc_start: 0.7042 (m-80) cc_final: 0.6567 (m-10) REVERT: A 881 LEU cc_start: 0.8436 (mt) cc_final: 0.8027 (mp) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.2375 time to fit residues: 74.7887 Evaluate side-chains 150 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 23 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 61 ASN A 120 GLN ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN A 249 GLN A 458 GLN A 592 GLN ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN A 865 GLN A 869 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6957 Z= 0.226 Angle : 0.946 32.993 9426 Z= 0.402 Chirality : 0.042 0.139 1131 Planarity : 0.004 0.045 1186 Dihedral : 5.258 92.474 948 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.14 % Allowed : 14.64 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.28), residues: 886 helix: 0.94 (0.24), residues: 452 sheet: -1.31 (0.49), residues: 111 loop : -1.42 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 795 HIS 0.003 0.001 HIS A 58 PHE 0.018 0.002 PHE A 538 TYR 0.023 0.002 TYR A 618 ARG 0.005 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4017 (mmm) cc_final: 0.3788 (mmm) REVERT: A 81 ASN cc_start: 0.6164 (t0) cc_final: 0.5817 (m-40) REVERT: A 110 ILE cc_start: 0.8644 (tt) cc_final: 0.8421 (tt) REVERT: A 172 ASP cc_start: 0.7990 (m-30) cc_final: 0.7762 (m-30) REVERT: A 452 TYR cc_start: 0.7116 (m-80) cc_final: 0.6487 (m-80) REVERT: A 510 TYR cc_start: 0.8931 (m-10) cc_final: 0.8539 (m-80) REVERT: A 568 MET cc_start: 0.8268 (tpt) cc_final: 0.6883 (tpt) REVERT: A 784 ILE cc_start: 0.9022 (tp) cc_final: 0.8814 (tp) REVERT: A 834 PHE cc_start: 0.7148 (m-80) cc_final: 0.6880 (m-10) REVERT: A 868 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.5044 (t80) REVERT: A 881 LEU cc_start: 0.8352 (mt) cc_final: 0.8091 (mp) REVERT: A 901 SER cc_start: 0.8844 (m) cc_final: 0.8519 (t) outliers start: 24 outliers final: 17 residues processed: 179 average time/residue: 0.2073 time to fit residues: 48.9389 Evaluate side-chains 155 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 GLN Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6957 Z= 0.220 Angle : 0.941 29.539 9426 Z= 0.395 Chirality : 0.042 0.164 1131 Planarity : 0.004 0.046 1186 Dihedral : 5.260 92.947 948 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.79 % Allowed : 17.78 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.29), residues: 886 helix: 1.29 (0.24), residues: 454 sheet: -1.43 (0.48), residues: 117 loop : -1.16 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 795 HIS 0.007 0.001 HIS A 98 PHE 0.012 0.001 PHE A 63 TYR 0.017 0.001 TYR A 618 ARG 0.005 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3922 (mmm) cc_final: 0.3703 (mmm) REVERT: A 81 ASN cc_start: 0.6121 (t0) cc_final: 0.5810 (m-40) REVERT: A 172 ASP cc_start: 0.8023 (m-30) cc_final: 0.7804 (m-30) REVERT: A 784 ILE cc_start: 0.9045 (tp) cc_final: 0.8843 (tp) REVERT: A 901 SER cc_start: 0.8884 (m) cc_final: 0.8542 (t) outliers start: 29 outliers final: 20 residues processed: 172 average time/residue: 0.1913 time to fit residues: 43.7187 Evaluate side-chains 159 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 54 optimal weight: 0.0770 chunk 81 optimal weight: 0.0980 chunk 86 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 120 GLN A 149 HIS A 249 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6957 Z= 0.163 Angle : 0.914 29.706 9426 Z= 0.377 Chirality : 0.041 0.136 1131 Planarity : 0.004 0.046 1186 Dihedral : 5.117 89.196 948 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.75 % Allowed : 21.70 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.30), residues: 886 helix: 1.68 (0.25), residues: 452 sheet: -1.26 (0.52), residues: 108 loop : -1.12 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 795 HIS 0.011 0.001 HIS A 98 PHE 0.012 0.001 PHE A 245 TYR 0.014 0.001 TYR A 618 ARG 0.003 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3880 (mmm) cc_final: 0.3631 (mmm) REVERT: A 81 ASN cc_start: 0.6110 (t0) cc_final: 0.5810 (m-40) REVERT: A 435 MET cc_start: 0.7321 (ptt) cc_final: 0.6959 (ptt) REVERT: A 587 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: A 784 ILE cc_start: 0.9054 (tp) cc_final: 0.8844 (tp) REVERT: A 901 SER cc_start: 0.8849 (m) cc_final: 0.8532 (t) outliers start: 21 outliers final: 16 residues processed: 173 average time/residue: 0.1864 time to fit residues: 43.3964 Evaluate side-chains 157 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 855 GLN Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.0000 chunk 73 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 overall best weight: 0.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 140 HIS ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6957 Z= 0.160 Angle : 0.913 29.667 9426 Z= 0.375 Chirality : 0.040 0.136 1131 Planarity : 0.004 0.046 1186 Dihedral : 5.045 86.713 948 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.40 % Allowed : 21.31 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 886 helix: 1.85 (0.25), residues: 451 sheet: -1.54 (0.54), residues: 97 loop : -0.95 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 72 HIS 0.011 0.001 HIS A 98 PHE 0.010 0.001 PHE A 245 TYR 0.013 0.001 TYR A 618 ARG 0.003 0.000 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3902 (mmm) cc_final: 0.3635 (mmm) REVERT: A 81 ASN cc_start: 0.5935 (t0) cc_final: 0.5657 (m-40) REVERT: A 435 MET cc_start: 0.7463 (ptt) cc_final: 0.7184 (ptt) REVERT: A 442 LEU cc_start: 0.7847 (mm) cc_final: 0.7425 (tp) REVERT: A 568 MET cc_start: 0.8445 (tpt) cc_final: 0.7554 (tpt) REVERT: A 587 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: A 784 ILE cc_start: 0.9066 (tp) cc_final: 0.8847 (tp) REVERT: A 901 SER cc_start: 0.8866 (m) cc_final: 0.8571 (t) outliers start: 26 outliers final: 16 residues processed: 163 average time/residue: 0.1712 time to fit residues: 38.0887 Evaluate side-chains 158 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 396 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.0060 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 364 HIS A 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6957 Z= 0.189 Angle : 0.921 29.537 9426 Z= 0.383 Chirality : 0.041 0.149 1131 Planarity : 0.004 0.045 1186 Dihedral : 5.070 85.729 948 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.61 % Allowed : 22.75 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 886 helix: 1.78 (0.25), residues: 460 sheet: -1.46 (0.54), residues: 97 loop : -0.85 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 72 HIS 0.012 0.001 HIS A 98 PHE 0.010 0.001 PHE A 245 TYR 0.012 0.001 TYR A 618 ARG 0.002 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.4262 (mmm) cc_final: 0.3989 (mmm) REVERT: A 81 ASN cc_start: 0.5955 (t0) cc_final: 0.5659 (m-40) REVERT: A 218 PHE cc_start: 0.6650 (m-80) cc_final: 0.6326 (m-80) REVERT: A 435 MET cc_start: 0.7453 (ptt) cc_final: 0.7195 (ptt) REVERT: A 442 LEU cc_start: 0.7863 (mm) cc_final: 0.7504 (tp) REVERT: A 587 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: A 732 MET cc_start: 0.8143 (mmm) cc_final: 0.7876 (mmt) REVERT: A 784 ILE cc_start: 0.9095 (tp) cc_final: 0.8888 (tp) REVERT: A 901 SER cc_start: 0.8921 (m) cc_final: 0.8642 (t) outliers start: 20 outliers final: 10 residues processed: 159 average time/residue: 0.1856 time to fit residues: 40.6221 Evaluate side-chains 146 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 856 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 0.0570 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 730 ASN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6957 Z= 0.203 Angle : 0.937 29.499 9426 Z= 0.390 Chirality : 0.042 0.154 1131 Planarity : 0.004 0.045 1186 Dihedral : 5.107 82.333 948 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.48 % Allowed : 25.10 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 886 helix: 1.86 (0.25), residues: 459 sheet: -1.45 (0.55), residues: 97 loop : -0.92 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 72 HIS 0.014 0.002 HIS A 98 PHE 0.009 0.001 PHE A 844 TYR 0.012 0.001 TYR A 618 ARG 0.003 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4424 (mmm) cc_final: 0.4127 (mmm) REVERT: A 81 ASN cc_start: 0.5998 (t0) cc_final: 0.5688 (m-40) REVERT: A 125 GLU cc_start: 0.5045 (pt0) cc_final: 0.4455 (pt0) REVERT: A 175 LEU cc_start: 0.7474 (mm) cc_final: 0.7157 (mp) REVERT: A 218 PHE cc_start: 0.6680 (m-80) cc_final: 0.6339 (m-80) REVERT: A 431 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 435 MET cc_start: 0.7481 (ptt) cc_final: 0.7277 (ptt) REVERT: A 442 LEU cc_start: 0.7936 (mm) cc_final: 0.7601 (tp) REVERT: A 587 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: A 732 MET cc_start: 0.8161 (mmm) cc_final: 0.7961 (mmt) REVERT: A 784 ILE cc_start: 0.9109 (tp) cc_final: 0.8903 (tp) REVERT: A 901 SER cc_start: 0.8920 (m) cc_final: 0.8661 (t) outliers start: 19 outliers final: 13 residues processed: 161 average time/residue: 0.1801 time to fit residues: 39.2610 Evaluate side-chains 150 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.0020 chunk 82 optimal weight: 0.0070 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 730 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6957 Z= 0.187 Angle : 0.939 29.590 9426 Z= 0.392 Chirality : 0.042 0.156 1131 Planarity : 0.004 0.045 1186 Dihedral : 5.068 80.144 948 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.01 % Allowed : 25.62 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.30), residues: 886 helix: 1.77 (0.25), residues: 465 sheet: -1.40 (0.55), residues: 97 loop : -0.80 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 72 HIS 0.008 0.001 HIS A 98 PHE 0.009 0.001 PHE A 702 TYR 0.012 0.001 TYR A 618 ARG 0.002 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4198 (mmm) cc_final: 0.3957 (mmm) REVERT: A 81 ASN cc_start: 0.5943 (t0) cc_final: 0.5646 (m-40) REVERT: A 218 PHE cc_start: 0.6583 (m-80) cc_final: 0.6267 (m-80) REVERT: A 264 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 274 PHE cc_start: 0.8472 (m-80) cc_final: 0.8263 (m-80) REVERT: A 442 LEU cc_start: 0.7933 (mm) cc_final: 0.7676 (tp) REVERT: A 587 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: A 784 ILE cc_start: 0.9121 (tp) cc_final: 0.8916 (tp) REVERT: A 881 LEU cc_start: 0.8338 (mp) cc_final: 0.8050 (mt) REVERT: A 901 SER cc_start: 0.8960 (m) cc_final: 0.8690 (t) outliers start: 23 outliers final: 16 residues processed: 151 average time/residue: 0.1968 time to fit residues: 41.9048 Evaluate side-chains 151 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 0.0270 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6957 Z= 0.183 Angle : 0.951 29.621 9426 Z= 0.397 Chirality : 0.042 0.149 1131 Planarity : 0.004 0.045 1186 Dihedral : 5.050 79.631 948 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.75 % Allowed : 26.14 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 886 helix: 1.87 (0.25), residues: 459 sheet: -1.42 (0.55), residues: 97 loop : -0.88 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 72 HIS 0.008 0.001 HIS A 98 PHE 0.009 0.001 PHE A 702 TYR 0.012 0.001 TYR A 618 ARG 0.003 0.000 ARG A 902 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4194 (mmm) cc_final: 0.3957 (mmm) REVERT: A 81 ASN cc_start: 0.5938 (t0) cc_final: 0.5639 (m-40) REVERT: A 175 LEU cc_start: 0.7699 (mm) cc_final: 0.7360 (mp) REVERT: A 218 PHE cc_start: 0.6528 (m-80) cc_final: 0.6307 (m-80) REVERT: A 264 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8409 (tt) REVERT: A 435 MET cc_start: 0.7031 (ptt) cc_final: 0.6636 (ptt) REVERT: A 442 LEU cc_start: 0.7838 (mm) cc_final: 0.7617 (tp) REVERT: A 587 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: A 784 ILE cc_start: 0.9117 (tp) cc_final: 0.8908 (tp) REVERT: A 901 SER cc_start: 0.9026 (m) cc_final: 0.8751 (t) outliers start: 21 outliers final: 17 residues processed: 154 average time/residue: 0.1773 time to fit residues: 37.2908 Evaluate side-chains 151 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 70 optimal weight: 0.0060 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 75 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 overall best weight: 0.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6957 Z= 0.174 Angle : 0.962 29.723 9426 Z= 0.403 Chirality : 0.042 0.142 1131 Planarity : 0.004 0.045 1186 Dihedral : 4.952 78.693 948 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.96 % Allowed : 27.32 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 886 helix: 1.89 (0.25), residues: 451 sheet: -1.22 (0.57), residues: 97 loop : -0.74 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.010 0.001 PHE A 702 TYR 0.012 0.001 TYR A 618 ARG 0.003 0.000 ARG A 902 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4226 (mmm) cc_final: 0.3992 (mmm) REVERT: A 81 ASN cc_start: 0.5858 (t0) cc_final: 0.5595 (m-40) REVERT: A 175 LEU cc_start: 0.7599 (mm) cc_final: 0.7396 (mm) REVERT: A 218 PHE cc_start: 0.6297 (m-80) cc_final: 0.6081 (m-10) REVERT: A 264 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8414 (tt) REVERT: A 435 MET cc_start: 0.6929 (ptt) cc_final: 0.6587 (ptt) REVERT: A 568 MET cc_start: 0.8450 (tpt) cc_final: 0.7680 (tpt) REVERT: A 587 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: A 707 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8158 (mm) REVERT: A 732 MET cc_start: 0.8050 (mmm) cc_final: 0.7832 (mmt) REVERT: A 760 ARG cc_start: 0.7684 (mpp80) cc_final: 0.7476 (ptp-170) REVERT: A 784 ILE cc_start: 0.9097 (tp) cc_final: 0.8867 (tp) REVERT: A 901 SER cc_start: 0.8996 (m) cc_final: 0.8684 (t) outliers start: 15 outliers final: 12 residues processed: 152 average time/residue: 0.1776 time to fit residues: 36.7042 Evaluate side-chains 145 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.0030 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137197 restraints weight = 11423.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139499 restraints weight = 7710.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140921 restraints weight = 5737.958| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6957 Z= 0.197 Angle : 0.975 29.649 9426 Z= 0.409 Chirality : 0.043 0.173 1131 Planarity : 0.004 0.045 1186 Dihedral : 4.973 77.445 948 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.22 % Allowed : 27.71 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 886 helix: 1.78 (0.25), residues: 462 sheet: -1.27 (0.56), residues: 97 loop : -0.65 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 72 HIS 0.005 0.001 HIS A 149 PHE 0.009 0.001 PHE A 63 TYR 0.012 0.001 TYR A 618 ARG 0.003 0.000 ARG A 902 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.74 seconds wall clock time: 35 minutes 37.90 seconds (2137.90 seconds total)