Starting phenix.real_space_refine on Tue Feb 13 15:40:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfy_33801/02_2024/7yfy_33801_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.124 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 4172 2.51 5 N 1172 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 806": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5898 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 697} Chain breaks: 3 Chain: "C" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 320 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.48, per 1000 atoms: 0.66 Number of scatterers: 6770 At special positions: 0 Unit cell: (73.916, 85.873, 114.135, 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 44 16.00 P 41 15.00 Mg 2 11.99 O 1339 8.00 N 1172 7.00 C 4172 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 - 3.50 Amino acid : False - 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: 3.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 11 sheets defined 33.4% alpha, 19.1% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 318 through 332 removed outlier: 4.325A pdb=" N VAL A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.806A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.590A pdb=" N GLN A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 541 through 550 removed outlier: 5.085A pdb=" N TRP A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.563A pdb=" N THR A 591 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 625 removed outlier: 3.754A pdb=" N MET A 613 " --> pdb=" O LYS A 610 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASP A 614 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN A 615 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 647 through 661 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 708 through 723 Processing helix chain 'A' and resid 779 through 801 removed outlier: 4.292A pdb=" N VAL A 783 " --> pdb=" O HIS A 779 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP A 784 " --> pdb=" O GLN A 780 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 4.427A pdb=" N LYS A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 837 removed outlier: 4.039A pdb=" N CYS A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA A 837 " --> pdb=" O LYS A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 927 removed outlier: 3.864A pdb=" N HIS A 927 " --> pdb=" O PHE A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 954 Processing helix chain 'A' and resid 963 through 966 removed outlier: 4.073A pdb=" N GLY A 966 " --> pdb=" O GLN A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 966' Processing sheet with id= A, first strand: chain 'A' and resid 221 through 223 Processing sheet with id= B, first strand: chain 'A' and resid 224 through 226 Processing sheet with id= C, first strand: chain 'A' and resid 228 through 231 removed outlier: 4.554A pdb=" N LEU A 372 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 276 through 279 removed outlier: 3.732A pdb=" N GLN A 240 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS A 308 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N HIS A 242 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A 306 " --> pdb=" O HIS A 242 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 244 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE A 304 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 347 through 349 Processing sheet with id= F, first strand: chain 'A' and resid 414 through 417 removed outlier: 4.103A pdb=" N SER A 414 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 427 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.676A pdb=" N ASP A 429 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 570 through 572 Processing sheet with id= I, first strand: chain 'A' and resid 638 through 642 removed outlier: 3.520A pdb=" N TYR A 608 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET A 666 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE A 607 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 668 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE A 670 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N CYS A 669 " --> pdb=" O PRO A 693 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN A 695 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 671 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 697 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 769 through 774 removed outlier: 3.549A pdb=" N VAL A 774 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 756 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 743 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS A 807 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 740 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL A 809 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET A 742 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR A 811 " --> pdb=" O MET A 742 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL A 744 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP A 813 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS A 844 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 810 " --> pdb=" O LYS A 844 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 846 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG A 812 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N PHE A 848 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 908 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 849 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N CYS A 906 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLN A 851 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR A 904 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 873 through 875 200 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1256 1.33 - 1.45: 1857 1.45 - 1.57: 3738 1.57 - 1.69: 80 1.69 - 1.81: 69 Bond restraints: 7000 Sorted by residual: bond pdb=" C2 OMC B 26 " pdb=" N3 OMC B 26 " ideal model delta sigma weight residual 1.491 1.351 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" N1 OMC B 26 " pdb=" C6 OMC B 26 " ideal model delta sigma weight residual 1.455 1.337 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C5 OMC B 26 " pdb=" C6 OMC B 26 " ideal model delta sigma weight residual 1.488 1.389 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" N3 OMC B 26 " pdb=" C4 OMC B 26 " ideal model delta sigma weight residual 1.448 1.350 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C4 OMC B 26 " pdb=" N4 OMC B 26 " ideal model delta sigma weight residual 1.452 1.356 0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 6995 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.03: 302 105.03 - 112.27: 3575 112.27 - 119.51: 2457 119.51 - 126.74: 3138 126.74 - 133.98: 203 Bond angle restraints: 9675 Sorted by residual: angle pdb=" N ASN A 422 " pdb=" CA ASN A 422 " pdb=" C ASN A 422 " ideal model delta sigma weight residual 113.23 105.49 7.74 1.24e+00 6.50e-01 3.90e+01 angle pdb=" C LYS A 506 " pdb=" CA LYS A 506 " pdb=" CB LYS A 506 " ideal model delta sigma weight residual 110.88 102.33 8.55 1.57e+00 4.06e-01 2.97e+01 angle pdb=" C3' OMC B 26 " pdb=" C2' OMC B 26 " pdb=" C1' OMC B 26 " ideal model delta sigma weight residual 101.50 106.27 -4.77 1.00e+00 1.00e+00 2.27e+01 angle pdb=" C CYS A 317 " pdb=" N ILE A 318 " pdb=" CA ILE A 318 " ideal model delta sigma weight residual 120.33 124.00 -3.67 8.00e-01 1.56e+00 2.11e+01 angle pdb=" N TYR A 420 " pdb=" CA TYR A 420 " pdb=" C TYR A 420 " ideal model delta sigma weight residual 112.34 106.92 5.42 1.30e+00 5.92e-01 1.74e+01 ... (remaining 9670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 4032 35.22 - 70.44: 212 70.44 - 105.66: 25 105.66 - 140.87: 0 140.87 - 176.09: 2 Dihedral angle restraints: 4271 sinusoidal: 2122 harmonic: 2149 Sorted by residual: dihedral pdb=" O4' U B 20 " pdb=" C1' U B 20 " pdb=" N1 U B 20 " pdb=" C2 U B 20 " ideal model delta sinusoidal sigma weight residual 232.00 55.91 176.09 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B 19 " pdb=" C1' C B 19 " pdb=" N1 C B 19 " pdb=" C2 C B 19 " ideal model delta sinusoidal sigma weight residual 232.00 60.07 171.93 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U B 21 " pdb=" C1' U B 21 " pdb=" N1 U B 21 " pdb=" C2 U B 21 " ideal model delta sinusoidal sigma weight residual -128.00 -57.44 -70.56 1 1.70e+01 3.46e-03 2.22e+01 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 907 0.056 - 0.112: 179 0.112 - 0.168: 39 0.168 - 0.224: 2 0.224 - 0.280: 1 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA LYS A 506 " pdb=" N LYS A 506 " pdb=" C LYS A 506 " pdb=" CB LYS A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA ARG A 895 " pdb=" N ARG A 895 " pdb=" C ARG A 895 " pdb=" CB ARG A 895 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 1125 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC B 26 " 0.466 2.00e-02 2.50e+03 4.49e-01 4.53e+03 pdb=" C4' OMC B 26 " -0.364 2.00e-02 2.50e+03 pdb=" O4' OMC B 26 " -0.805 2.00e-02 2.50e+03 pdb=" C3' OMC B 26 " 0.451 2.00e-02 2.50e+03 pdb=" O3' OMC B 26 " -0.159 2.00e-02 2.50e+03 pdb=" C2' OMC B 26 " 0.451 2.00e-02 2.50e+03 pdb=" O2' OMC B 26 " -0.156 2.00e-02 2.50e+03 pdb=" C1' OMC B 26 " -0.361 2.00e-02 2.50e+03 pdb=" N1 OMC B 26 " 0.477 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 704 " -0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 705 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 705 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 705 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 241 " 0.010 2.00e-02 2.50e+03 1.65e-02 5.42e+00 pdb=" CG TYR A 241 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 241 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 241 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 241 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 241 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 241 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 241 " -0.002 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 28 2.51 - 3.11: 4798 3.11 - 3.71: 10425 3.71 - 4.30: 14614 4.30 - 4.90: 23510 Nonbonded interactions: 53375 Sorted by model distance: nonbonded pdb=" OD2 ASP A 743 " pdb="MG MG A1002 " model vdw 1.918 2.170 nonbonded pdb=" OP1 A B 3 " pdb="MG MG A1001 " model vdw 1.977 2.170 nonbonded pdb=" OXT LEU A 971 " pdb="MG MG A1001 " model vdw 2.055 2.170 nonbonded pdb=" O2' G B 22 " pdb=" N2 G B 23 " model vdw 2.142 2.520 nonbonded pdb=" OE1 GLN A 718 " pdb="MG MG A1001 " model vdw 2.196 2.170 ... (remaining 53370 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 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: 0.300 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: 1.860 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.770 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 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 : 0.006 0.140 7000 Z= 0.343 Angle : 0.859 8.549 9675 Z= 0.483 Chirality : 0.049 0.280 1128 Planarity : 0.015 0.449 1072 Dihedral : 19.570 176.092 2879 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 1.35 % Allowed : 15.32 % Favored : 83.33 % Cbeta Deviations : 0.14 % 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: -1.34 (0.30), residues: 726 helix: 0.82 (0.34), residues: 224 sheet: -1.22 (0.38), residues: 168 loop : -1.91 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.007 0.001 HIS A 526 PHE 0.015 0.002 PHE A 325 TYR 0.039 0.002 TYR A 241 ARG 0.005 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.7284 (mmt) cc_final: 0.6856 (mmm) REVERT: A 496 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7562 (p) REVERT: A 706 THR cc_start: 0.7834 (p) cc_final: 0.7632 (p) REVERT: A 737 LEU cc_start: 0.7669 (pt) cc_final: 0.7445 (pt) REVERT: A 752 MET cc_start: 0.5399 (tpt) cc_final: 0.4975 (tmm) REVERT: A 753 ARG cc_start: 0.6931 (mmm-85) cc_final: 0.6708 (mmt180) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 0.2193 time to fit residues: 26.0187 Evaluate side-chains 76 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 509 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 0.0170 chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7000 Z= 0.218 Angle : 0.702 12.511 9675 Z= 0.385 Chirality : 0.044 0.169 1128 Planarity : 0.006 0.113 1072 Dihedral : 20.210 175.041 1417 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer: Outliers : 3.30 % Allowed : 15.77 % Favored : 80.93 % 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: -0.97 (0.31), residues: 726 helix: 1.20 (0.35), residues: 230 sheet: -1.04 (0.39), residues: 168 loop : -1.77 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.006 0.001 HIS A 526 PHE 0.010 0.001 PHE A 320 TYR 0.016 0.001 TYR A 454 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.736 Fit side-chains REVERT: A 258 MET cc_start: 0.7163 (mmt) cc_final: 0.6832 (mmm) REVERT: A 335 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6611 (mmmt) REVERT: A 361 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6716 (p90) REVERT: A 450 PHE cc_start: 0.5166 (OUTLIER) cc_final: 0.4808 (t80) REVERT: A 752 MET cc_start: 0.5293 (tpt) cc_final: 0.4831 (tmm) REVERT: A 753 ARG cc_start: 0.7095 (mmm-85) cc_final: 0.6888 (mmt180) REVERT: A 876 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5516 (p0) outliers start: 22 outliers final: 11 residues processed: 99 average time/residue: 0.1980 time to fit residues: 26.0048 Evaluate side-chains 83 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7000 Z= 0.229 Angle : 0.684 12.942 9675 Z= 0.376 Chirality : 0.044 0.177 1128 Planarity : 0.006 0.113 1072 Dihedral : 20.025 176.824 1410 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.15 % Allowed : 18.92 % Favored : 77.93 % 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: -0.86 (0.31), residues: 726 helix: 1.26 (0.35), residues: 230 sheet: -0.89 (0.39), residues: 168 loop : -1.75 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 930 HIS 0.006 0.001 HIS A 526 PHE 0.012 0.001 PHE A 325 TYR 0.013 0.001 TYR A 454 ARG 0.007 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.743 Fit side-chains REVERT: A 258 MET cc_start: 0.7177 (mmt) cc_final: 0.6955 (mmm) REVERT: A 269 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7060 (p) REVERT: A 361 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.6521 (p90) REVERT: A 396 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.5869 (t80) REVERT: A 450 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4910 (t80) REVERT: A 706 THR cc_start: 0.7757 (p) cc_final: 0.7516 (p) REVERT: A 876 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.5729 (p0) outliers start: 21 outliers final: 11 residues processed: 88 average time/residue: 0.1597 time to fit residues: 20.2788 Evaluate side-chains 79 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7000 Z= 0.198 Angle : 0.663 12.678 9675 Z= 0.364 Chirality : 0.042 0.173 1128 Planarity : 0.005 0.112 1072 Dihedral : 19.945 177.830 1410 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.05 % Allowed : 18.32 % Favored : 77.63 % 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: -0.68 (0.31), residues: 726 helix: 1.45 (0.36), residues: 223 sheet: -0.80 (0.39), residues: 168 loop : -1.60 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 930 HIS 0.004 0.001 HIS A 526 PHE 0.012 0.001 PHE A 325 TYR 0.011 0.001 TYR A 454 ARG 0.002 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.732 Fit side-chains REVERT: A 239 TYR cc_start: 0.7113 (m-10) cc_final: 0.6506 (m-10) REVERT: A 258 MET cc_start: 0.7177 (mmt) cc_final: 0.6960 (mmm) REVERT: A 269 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7079 (p) REVERT: A 361 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6388 (p90) REVERT: A 396 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.5871 (t80) REVERT: A 450 PHE cc_start: 0.5345 (OUTLIER) cc_final: 0.4948 (t80) REVERT: A 568 MET cc_start: 0.6935 (mtp) cc_final: 0.6661 (mtm) REVERT: A 706 THR cc_start: 0.7907 (p) cc_final: 0.7685 (p) REVERT: A 876 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.5684 (p0) outliers start: 27 outliers final: 15 residues processed: 88 average time/residue: 0.1425 time to fit residues: 18.4014 Evaluate side-chains 84 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.0370 chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7000 Z= 0.273 Angle : 0.703 12.598 9675 Z= 0.384 Chirality : 0.044 0.166 1128 Planarity : 0.006 0.112 1072 Dihedral : 19.934 179.901 1410 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.65 % Allowed : 18.47 % Favored : 76.88 % 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: -1.06 (0.31), residues: 726 helix: 1.11 (0.35), residues: 228 sheet: -0.93 (0.39), residues: 174 loop : -1.92 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 930 HIS 0.007 0.001 HIS A 526 PHE 0.015 0.002 PHE A 325 TYR 0.018 0.002 TYR A 425 ARG 0.003 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.784 Fit side-chains REVERT: A 239 TYR cc_start: 0.7163 (m-10) cc_final: 0.6465 (m-10) REVERT: A 242 HIS cc_start: 0.6974 (m-70) cc_final: 0.6724 (m-70) REVERT: A 258 MET cc_start: 0.7240 (mmt) cc_final: 0.7019 (mmm) REVERT: A 269 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7069 (p) REVERT: A 361 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.6418 (p90) REVERT: A 396 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5841 (t80) REVERT: A 427 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7317 (tp) REVERT: A 441 VAL cc_start: 0.4375 (OUTLIER) cc_final: 0.4066 (p) REVERT: A 450 PHE cc_start: 0.5409 (OUTLIER) cc_final: 0.4895 (t80) REVERT: A 505 MET cc_start: 0.8084 (tpp) cc_final: 0.7841 (tpp) REVERT: A 876 ASP cc_start: 0.6375 (OUTLIER) cc_final: 0.5832 (p0) REVERT: A 964 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7793 (mt) outliers start: 31 outliers final: 19 residues processed: 95 average time/residue: 0.1556 time to fit residues: 21.2343 Evaluate side-chains 91 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7000 Z= 0.203 Angle : 0.665 12.522 9675 Z= 0.365 Chirality : 0.043 0.241 1128 Planarity : 0.005 0.112 1072 Dihedral : 19.811 179.274 1410 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.50 % Allowed : 19.67 % Favored : 75.83 % 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: -0.94 (0.31), residues: 726 helix: 1.23 (0.36), residues: 230 sheet: -0.90 (0.39), residues: 174 loop : -1.86 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.004 0.001 HIS A 526 PHE 0.012 0.001 PHE A 325 TYR 0.018 0.001 TYR A 770 ARG 0.002 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 68 time to evaluate : 0.719 Fit side-chains REVERT: A 239 TYR cc_start: 0.7071 (m-10) cc_final: 0.6476 (m-10) REVERT: A 258 MET cc_start: 0.7264 (mmt) cc_final: 0.7047 (mmm) REVERT: A 269 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7127 (p) REVERT: A 329 MET cc_start: 0.7263 (mmm) cc_final: 0.6973 (mpp) REVERT: A 361 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.6355 (p90) REVERT: A 396 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5822 (t80) REVERT: A 441 VAL cc_start: 0.4142 (OUTLIER) cc_final: 0.3783 (p) REVERT: A 450 PHE cc_start: 0.5309 (OUTLIER) cc_final: 0.4809 (t80) REVERT: A 964 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7689 (mt) outliers start: 30 outliers final: 16 residues processed: 92 average time/residue: 0.1434 time to fit residues: 19.3866 Evaluate side-chains 89 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7000 Z= 0.290 Angle : 0.707 13.020 9675 Z= 0.384 Chirality : 0.044 0.196 1128 Planarity : 0.006 0.112 1072 Dihedral : 19.822 178.209 1410 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.95 % Allowed : 19.22 % Favored : 75.83 % 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: -1.16 (0.31), residues: 726 helix: 1.14 (0.36), residues: 228 sheet: -1.12 (0.38), residues: 179 loop : -1.99 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 586 HIS 0.006 0.001 HIS A 526 PHE 0.013 0.001 PHE A 325 TYR 0.014 0.002 TYR A 650 ARG 0.003 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 71 time to evaluate : 0.763 Fit side-chains REVERT: A 239 TYR cc_start: 0.7087 (m-10) cc_final: 0.6842 (m-80) REVERT: A 258 MET cc_start: 0.7280 (mmt) cc_final: 0.7034 (mmm) REVERT: A 269 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7030 (p) REVERT: A 300 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6213 (mp) REVERT: A 329 MET cc_start: 0.7317 (mmm) cc_final: 0.7040 (mpp) REVERT: A 361 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6518 (p90) REVERT: A 396 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.5816 (t80) REVERT: A 450 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4676 (t80) REVERT: A 505 MET cc_start: 0.8039 (tpp) cc_final: 0.7577 (tpp) REVERT: A 876 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.5895 (p0) REVERT: A 964 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7691 (mt) outliers start: 33 outliers final: 21 residues processed: 97 average time/residue: 0.1437 time to fit residues: 20.5349 Evaluate side-chains 98 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 70 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7000 Z= 0.181 Angle : 0.664 13.417 9675 Z= 0.362 Chirality : 0.043 0.185 1128 Planarity : 0.005 0.112 1072 Dihedral : 19.724 178.261 1410 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.05 % Allowed : 21.47 % Favored : 74.47 % 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: -1.03 (0.31), residues: 726 helix: 1.30 (0.36), residues: 230 sheet: -1.13 (0.38), residues: 181 loop : -1.92 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.003 0.001 HIS A 927 PHE 0.012 0.001 PHE A 325 TYR 0.018 0.001 TYR A 770 ARG 0.001 0.000 ARG A 812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 0.737 Fit side-chains REVERT: A 239 TYR cc_start: 0.7021 (m-10) cc_final: 0.6460 (m-10) REVERT: A 258 MET cc_start: 0.7264 (mmt) cc_final: 0.7053 (mmm) REVERT: A 269 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7182 (p) REVERT: A 361 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6356 (p90) REVERT: A 450 PHE cc_start: 0.5401 (OUTLIER) cc_final: 0.4901 (t80) REVERT: A 505 MET cc_start: 0.8093 (tpp) cc_final: 0.7665 (tpp) REVERT: A 876 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5492 (p0) REVERT: A 964 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7670 (mt) outliers start: 27 outliers final: 18 residues processed: 95 average time/residue: 0.1528 time to fit residues: 21.2226 Evaluate side-chains 95 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7000 Z= 0.277 Angle : 0.707 13.749 9675 Z= 0.382 Chirality : 0.044 0.181 1128 Planarity : 0.006 0.112 1072 Dihedral : 19.745 177.223 1410 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.80 % Allowed : 20.72 % Favored : 74.47 % 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: -1.16 (0.31), residues: 726 helix: 1.20 (0.36), residues: 228 sheet: -1.13 (0.38), residues: 179 loop : -2.03 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.006 0.001 HIS A 892 PHE 0.013 0.001 PHE A 325 TYR 0.013 0.002 TYR A 650 ARG 0.002 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 0.748 Fit side-chains REVERT: A 258 MET cc_start: 0.7321 (mmt) cc_final: 0.7090 (mmm) REVERT: A 269 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7136 (p) REVERT: A 300 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6193 (mp) REVERT: A 361 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6504 (p90) REVERT: A 450 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.4913 (t80) REVERT: A 505 MET cc_start: 0.8099 (tpp) cc_final: 0.7665 (tpp) REVERT: A 876 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5765 (p0) REVERT: A 964 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7678 (mt) outliers start: 32 outliers final: 25 residues processed: 98 average time/residue: 0.1358 time to fit residues: 19.8054 Evaluate side-chains 101 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 18 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7000 Z= 0.221 Angle : 0.697 14.136 9675 Z= 0.376 Chirality : 0.043 0.161 1128 Planarity : 0.005 0.112 1072 Dihedral : 19.720 177.152 1410 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.80 % Allowed : 21.47 % Favored : 73.72 % 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: -1.13 (0.31), residues: 726 helix: 1.18 (0.36), residues: 230 sheet: -1.14 (0.38), residues: 180 loop : -1.98 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 586 HIS 0.004 0.001 HIS A 892 PHE 0.012 0.001 PHE A 325 TYR 0.011 0.002 TYR A 770 ARG 0.001 0.000 ARG A 675 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 0.731 Fit side-chains REVERT: A 258 MET cc_start: 0.7273 (mmt) cc_final: 0.7042 (mmm) REVERT: A 269 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7202 (p) REVERT: A 300 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6275 (mp) REVERT: A 361 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6477 (p90) REVERT: A 396 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.5796 (t80) REVERT: A 450 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.4961 (t80) REVERT: A 505 MET cc_start: 0.8112 (tpp) cc_final: 0.7605 (tpp) REVERT: A 623 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7154 (mm) REVERT: A 876 ASP cc_start: 0.6258 (OUTLIER) cc_final: 0.5813 (p0) REVERT: A 964 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7669 (mt) outliers start: 32 outliers final: 24 residues processed: 97 average time/residue: 0.1389 time to fit residues: 20.1085 Evaluate side-chains 103 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 71 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.208273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.157101 restraints weight = 8101.869| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.44 r_work: 0.3687 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7000 Z= 0.220 Angle : 0.691 14.158 9675 Z= 0.373 Chirality : 0.043 0.158 1128 Planarity : 0.005 0.112 1072 Dihedral : 19.632 176.376 1410 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.95 % Allowed : 21.32 % Favored : 73.72 % 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: -1.10 (0.31), residues: 726 helix: 1.21 (0.36), residues: 230 sheet: -1.12 (0.38), residues: 180 loop : -1.97 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 728 HIS 0.004 0.001 HIS A 892 PHE 0.012 0.001 PHE A 325 TYR 0.013 0.002 TYR A 608 ARG 0.002 0.000 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.27 seconds wall clock time: 30 minutes 8.67 seconds (1808.67 seconds total)