Starting phenix.real_space_refine on Sat Sep 28 00:47:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/09_2024/8d3u_27164_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/09_2024/8d3u_27164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/09_2024/8d3u_27164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/09_2024/8d3u_27164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/09_2024/8d3u_27164_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/09_2024/8d3u_27164_neut.cif" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9272 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 S 60 5.16 5 C 6462 2.51 5 N 1689 2.21 5 O 1903 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 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7521 Classifications: {'peptide': 971} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 929} Chain breaks: 1 Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2322 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.39, per 1000 atoms: 0.63 Number of scatterers: 10121 At special positions: 0 Unit cell: (143.59, 98.77, 131.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 60 16.00 P 2 15.00 Al 1 13.00 F 4 9.00 O 1903 8.00 N 1689 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 47.9% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.824A pdb=" N TYR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.541A pdb=" N GLN A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.720A pdb=" N CYS A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 110 Processing helix chain 'A' and resid 119 through 153 removed outlier: 3.587A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.873A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 304 Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 325 through 343 Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.927A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.774A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 456 through 464 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.716A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 697 Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 746 through 770 removed outlier: 3.585A pdb=" N THR A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.652A pdb=" N ILE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 847 through 867 Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.581A pdb=" N LEU A 873 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.804A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.761A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.872A pdb=" N ALA A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.852A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS A 980 " --> pdb=" O TRP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'B' and resid 34 through 61 removed outlier: 3.633A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.509A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.825A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.719A pdb=" N ASP B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 58 removed outlier: 4.082A pdb=" N ILE G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU G 57 " --> pdb=" O ILE G 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.902A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS A 239 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU A 241 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N CYS A 201 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 247 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE A 195 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.561A pdb=" N ASP A 187 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS A 239 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU A 241 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N CYS A 201 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 247 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE A 195 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.762A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 389 removed outlier: 3.685A pdb=" N THR A 377 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 580 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 541 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 480 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU A 469 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 482 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 389 removed outlier: 3.685A pdb=" N THR A 377 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS A 508 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE A 575 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 510 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY A 577 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 653 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.727A pdb=" N ALA B 260 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.618A pdb=" N PHE B 90 " --> pdb=" O GLU B 300 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3303 1.35 - 1.46: 2297 1.46 - 1.58: 4634 1.58 - 1.70: 5 1.70 - 1.82: 92 Bond restraints: 10331 Sorted by residual: bond pdb=" C3' ADP A1101 " pdb=" C4' ADP A1101 " ideal model delta sigma weight residual 1.524 1.305 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C4' ADP A1101 " pdb=" O4' ADP A1101 " ideal model delta sigma weight residual 1.426 1.614 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" C4 ADP A1101 " pdb=" C5 ADP A1101 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" F2 ALF A1102 " pdb="AL ALF A1102 " ideal model delta sigma weight residual 1.685 1.808 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1' ADP A1101 " pdb=" O4' ADP A1101 " ideal model delta sigma weight residual 1.426 1.305 0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 10326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.99: 13996 13.99 - 27.98: 7 27.98 - 41.97: 0 41.97 - 55.96: 0 55.96 - 69.95: 2 Bond angle restraints: 14005 Sorted by residual: angle pdb=" F3 ALF A1102 " pdb="AL ALF A1102 " pdb=" F4 ALF A1102 " ideal model delta sigma weight residual 109.63 179.58 -69.95 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F1 ALF A1102 " pdb="AL ALF A1102 " pdb=" F2 ALF A1102 " ideal model delta sigma weight residual 108.68 178.40 -69.72 3.00e+00 1.11e-01 5.40e+02 angle pdb=" N GLU A 33 " pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta sigma weight residual 110.50 130.21 -19.71 1.70e+00 3.46e-01 1.34e+02 angle pdb=" C1' ADP A1101 " pdb=" N9 ADP A1101 " pdb=" C8 ADP A1101 " ideal model delta sigma weight residual 126.00 104.64 21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" F2 ALF A1102 " pdb="AL ALF A1102 " pdb=" F4 ALF A1102 " ideal model delta sigma weight residual 110.21 89.68 20.53 3.00e+00 1.11e-01 4.68e+01 ... (remaining 14000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 5909 31.31 - 62.61: 277 62.61 - 93.92: 27 93.92 - 125.22: 0 125.22 - 156.53: 2 Dihedral angle restraints: 6215 sinusoidal: 2513 harmonic: 3702 Sorted by residual: dihedral pdb=" N GLU A 33 " pdb=" C GLU A 33 " pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta harmonic sigma weight residual 122.80 151.63 -28.83 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 49 " pdb=" CB CYS A 49 " ideal model delta sinusoidal sigma weight residual 93.00 6.73 86.27 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" C GLU A 33 " pdb=" N GLU A 33 " pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta harmonic sigma weight residual -122.60 -144.64 22.04 0 2.50e+00 1.60e-01 7.77e+01 ... (remaining 6212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1577 0.219 - 0.439: 1 0.439 - 0.658: 0 0.658 - 0.877: 0 0.877 - 1.097: 1 Chirality restraints: 1579 Sorted by residual: chirality pdb=" CA GLU A 33 " pdb=" N GLU A 33 " pdb=" C GLU A 33 " pdb=" CB GLU A 33 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CB ILE A 926 " pdb=" CA ILE A 926 " pdb=" CG1 ILE A 926 " pdb=" CG2 ILE A 926 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA MET B 121 " pdb=" N MET B 121 " pdb=" C MET B 121 " pdb=" CB MET B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1576 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 66 " -0.043 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 67 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 120 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C ASP B 120 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP B 120 " 0.015 2.00e-02 2.50e+03 pdb=" N MET B 121 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 610 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO A 611 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.027 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 2 2.09 - 2.79: 2662 2.79 - 3.50: 14548 3.50 - 4.20: 23013 4.20 - 4.90: 41948 Nonbonded interactions: 82173 Sorted by model distance: nonbonded pdb=" O TYR G 34 " pdb=" N THR G 36 " model vdw 1.392 3.120 nonbonded pdb=" O TYR G 34 " pdb=" N LEU G 37 " model vdw 2.087 3.120 nonbonded pdb=" O2B ADP A1101 " pdb=" F2 ALF A1102 " model vdw 2.149 2.990 nonbonded pdb=" O THR A 368 " pdb=" F3 ALF A1102 " model vdw 2.162 2.990 nonbonded pdb=" N ASP G 33 " pdb=" OD1 ASP G 33 " model vdw 2.174 3.120 ... (remaining 82168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.300 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.005 0.219 10331 Z= 0.363 Angle : 1.154 69.952 14005 Z= 0.481 Chirality : 0.050 1.097 1579 Planarity : 0.004 0.064 1804 Dihedral : 17.659 156.527 3830 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 0.63 % Allowed : 27.89 % Favored : 71.48 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % 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: 0.50 (0.24), residues: 1279 helix: 1.81 (0.23), residues: 539 sheet: -0.31 (0.51), residues: 121 loop : -0.88 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.002 0.001 HIS A 656 PHE 0.017 0.001 PHE G 44 TYR 0.014 0.001 TYR A 859 ARG 0.002 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ASP cc_start: 0.2422 (OUTLIER) cc_final: 0.2052 (p0) outliers start: 7 outliers final: 3 residues processed: 136 average time/residue: 0.1854 time to fit residues: 37.9512 Evaluate side-chains 132 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain G residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.0050 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 223 HIS A 283 GLN A 479 GLN A 530 ASN A 554 GLN A 866 ASN A 920 GLN A 936 GLN B 234 ASN B 265 ASN G 31 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10331 Z= 0.191 Angle : 0.592 9.704 14005 Z= 0.300 Chirality : 0.042 0.169 1579 Planarity : 0.004 0.046 1804 Dihedral : 6.276 109.974 1404 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 2.71 % Allowed : 25.54 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1279 helix: 1.84 (0.23), residues: 557 sheet: -0.53 (0.47), residues: 141 loop : -0.83 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS G 31 PHE 0.017 0.001 PHE A 783 TYR 0.013 0.001 TYR A 859 ARG 0.003 0.000 ARG A 877 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7879 (m) cc_final: 0.7435 (t) REVERT: A 90 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7244 (t80) REVERT: A 568 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5746 (m-80) REVERT: G 35 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7880 (tm-30) outliers start: 30 outliers final: 12 residues processed: 166 average time/residue: 0.1699 time to fit residues: 43.2392 Evaluate side-chains 146 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 0.0020 chunk 93 optimal weight: 0.7980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 476 ASN A 479 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10331 Z= 0.153 Angle : 0.555 8.878 14005 Z= 0.282 Chirality : 0.041 0.162 1579 Planarity : 0.004 0.048 1804 Dihedral : 6.138 114.540 1396 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.53 % Allowed : 25.18 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.65 (0.24), residues: 1279 helix: 1.95 (0.22), residues: 555 sheet: -0.58 (0.48), residues: 133 loop : -0.81 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.002 0.001 HIS A 656 PHE 0.014 0.001 PHE A 783 TYR 0.012 0.001 TYR A 859 ARG 0.006 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7813 (m) cc_final: 0.7391 (t) REVERT: A 568 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5646 (m-80) REVERT: A 842 MET cc_start: 0.9091 (mmm) cc_final: 0.8808 (tpt) REVERT: G 35 GLN cc_start: 0.8053 (tm-30) cc_final: 0.6972 (tm-30) outliers start: 28 outliers final: 10 residues processed: 172 average time/residue: 0.1678 time to fit residues: 44.4087 Evaluate side-chains 144 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 264 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 205 ASN B 234 ASN B 241 GLN G 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10331 Z= 0.350 Angle : 0.660 9.055 14005 Z= 0.334 Chirality : 0.045 0.175 1579 Planarity : 0.005 0.045 1804 Dihedral : 6.420 122.197 1396 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.14 % Rotamer: Outliers : 4.60 % Allowed : 25.36 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.42 (0.24), residues: 1279 helix: 1.65 (0.22), residues: 565 sheet: -0.65 (0.46), residues: 137 loop : -0.86 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.004 0.001 HIS A 483 PHE 0.022 0.002 PHE A 783 TYR 0.018 0.002 TYR A 859 ARG 0.005 0.001 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7980 (m) cc_final: 0.7609 (t) REVERT: A 120 LEU cc_start: 0.7879 (pt) cc_final: 0.7672 (pt) REVERT: A 305 TYR cc_start: 0.6989 (m-80) cc_final: 0.6259 (m-80) REVERT: A 418 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7824 (t) REVERT: A 568 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6061 (m-80) REVERT: A 750 THR cc_start: 0.9084 (p) cc_final: 0.8871 (t) REVERT: A 901 ARG cc_start: 0.9177 (ptp90) cc_final: 0.8597 (ptt90) REVERT: B 99 GLU cc_start: 0.7883 (tp30) cc_final: 0.7636 (tp30) REVERT: B 242 TYR cc_start: 0.8594 (m-80) cc_final: 0.8313 (m-80) outliers start: 51 outliers final: 29 residues processed: 174 average time/residue: 0.1678 time to fit residues: 45.3541 Evaluate side-chains 151 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN B 262 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10331 Z= 0.193 Angle : 0.587 7.950 14005 Z= 0.295 Chirality : 0.043 0.176 1579 Planarity : 0.004 0.046 1804 Dihedral : 6.235 120.904 1396 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 2.62 % Allowed : 27.26 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.55 (0.25), residues: 1279 helix: 1.90 (0.23), residues: 555 sheet: -0.76 (0.45), residues: 145 loop : -0.86 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.003 0.001 HIS A 483 PHE 0.022 0.001 PHE A 291 TYR 0.014 0.001 TYR A 859 ARG 0.004 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7907 (m) cc_final: 0.7504 (t) REVERT: A 305 TYR cc_start: 0.6796 (m-80) cc_final: 0.6154 (m-80) REVERT: A 418 CYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7770 (t) REVERT: A 568 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5976 (m-80) REVERT: A 842 MET cc_start: 0.9116 (mmm) cc_final: 0.8789 (tpt) REVERT: A 901 ARG cc_start: 0.9010 (ptp90) cc_final: 0.8428 (ptt90) REVERT: B 32 TRP cc_start: 0.7002 (t-100) cc_final: 0.6696 (t-100) REVERT: B 87 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: B 99 GLU cc_start: 0.7891 (tp30) cc_final: 0.7648 (tp30) REVERT: B 242 TYR cc_start: 0.8483 (m-80) cc_final: 0.8167 (m-80) outliers start: 29 outliers final: 21 residues processed: 156 average time/residue: 0.1743 time to fit residues: 41.9916 Evaluate side-chains 154 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 0.0050 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10331 Z= 0.204 Angle : 0.586 8.447 14005 Z= 0.292 Chirality : 0.043 0.181 1579 Planarity : 0.004 0.047 1804 Dihedral : 6.161 120.845 1396 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 3.52 % Allowed : 26.26 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.58 (0.25), residues: 1279 helix: 1.91 (0.23), residues: 555 sheet: -0.75 (0.45), residues: 145 loop : -0.82 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.003 0.001 HIS A 483 PHE 0.017 0.001 PHE A 783 TYR 0.015 0.001 TYR A 859 ARG 0.003 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7903 (m) cc_final: 0.7510 (t) REVERT: A 305 TYR cc_start: 0.6786 (m-80) cc_final: 0.6124 (m-80) REVERT: A 418 CYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7764 (t) REVERT: A 568 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: A 569 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7176 (p) REVERT: A 822 MET cc_start: 0.8502 (mmm) cc_final: 0.8140 (tpp) REVERT: A 842 MET cc_start: 0.9129 (mmm) cc_final: 0.8840 (tpt) REVERT: A 901 ARG cc_start: 0.8988 (ptp90) cc_final: 0.8368 (ptt90) REVERT: B 87 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: B 99 GLU cc_start: 0.7899 (tp30) cc_final: 0.7680 (tp30) REVERT: B 242 TYR cc_start: 0.8478 (m-80) cc_final: 0.8174 (m-80) outliers start: 39 outliers final: 24 residues processed: 169 average time/residue: 0.1647 time to fit residues: 43.0776 Evaluate side-chains 153 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain G residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 77 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 476 ASN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10331 Z= 0.194 Angle : 0.587 10.312 14005 Z= 0.293 Chirality : 0.043 0.212 1579 Planarity : 0.004 0.047 1804 Dihedral : 6.076 119.231 1396 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 3.07 % Allowed : 26.99 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.63 (0.25), residues: 1279 helix: 1.93 (0.23), residues: 556 sheet: -0.72 (0.46), residues: 140 loop : -0.78 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 79 HIS 0.003 0.001 HIS A 483 PHE 0.017 0.001 PHE A 783 TYR 0.015 0.001 TYR A 859 ARG 0.002 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7869 (m) cc_final: 0.7479 (t) REVERT: A 418 CYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7747 (t) REVERT: A 568 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5981 (m-80) REVERT: A 569 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7225 (p) REVERT: A 822 MET cc_start: 0.8536 (mmm) cc_final: 0.8149 (tpp) REVERT: A 842 MET cc_start: 0.9124 (mmm) cc_final: 0.8842 (tpt) REVERT: B 32 TRP cc_start: 0.6951 (t-100) cc_final: 0.6631 (t-100) REVERT: B 87 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: B 242 TYR cc_start: 0.8454 (m-80) cc_final: 0.8153 (m-80) outliers start: 34 outliers final: 25 residues processed: 164 average time/residue: 0.1739 time to fit residues: 44.3799 Evaluate side-chains 151 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain G residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 84 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10331 Z= 0.155 Angle : 0.593 13.424 14005 Z= 0.292 Chirality : 0.042 0.229 1579 Planarity : 0.004 0.048 1804 Dihedral : 5.775 110.224 1396 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.71 % Allowed : 27.26 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.72 (0.25), residues: 1279 helix: 2.01 (0.23), residues: 555 sheet: -0.60 (0.47), residues: 142 loop : -0.76 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 79 HIS 0.003 0.001 HIS A 483 PHE 0.014 0.001 PHE A 783 TYR 0.013 0.001 TYR A 859 ARG 0.002 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7920 (m) cc_final: 0.7546 (t) REVERT: A 418 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7732 (t) REVERT: A 568 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5783 (m-80) REVERT: A 822 MET cc_start: 0.8388 (mmm) cc_final: 0.8116 (tpp) REVERT: A 842 MET cc_start: 0.9115 (mmm) cc_final: 0.8868 (tpt) REVERT: B 32 TRP cc_start: 0.6865 (t-100) cc_final: 0.6539 (t-100) REVERT: B 87 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: B 99 GLU cc_start: 0.7792 (tp30) cc_final: 0.7551 (tp30) outliers start: 30 outliers final: 18 residues processed: 165 average time/residue: 0.1762 time to fit residues: 45.0704 Evaluate side-chains 147 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 264 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10331 Z= 0.219 Angle : 0.620 14.155 14005 Z= 0.307 Chirality : 0.043 0.226 1579 Planarity : 0.004 0.048 1804 Dihedral : 5.698 107.884 1396 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 2.62 % Allowed : 27.35 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.66 (0.25), residues: 1279 helix: 1.97 (0.23), residues: 554 sheet: -0.69 (0.45), residues: 148 loop : -0.78 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 79 HIS 0.003 0.001 HIS A 199 PHE 0.017 0.001 PHE A 783 TYR 0.015 0.001 TYR A 859 ARG 0.003 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 CYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7798 (t) REVERT: A 497 MET cc_start: 0.8269 (tpp) cc_final: 0.8061 (mmm) REVERT: A 568 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: A 569 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7204 (p) REVERT: A 754 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: A 842 MET cc_start: 0.9127 (mmm) cc_final: 0.8871 (tpt) REVERT: A 950 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 87 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: B 99 GLU cc_start: 0.7753 (tp30) cc_final: 0.7538 (tp30) REVERT: B 242 TYR cc_start: 0.8451 (m-80) cc_final: 0.8159 (m-80) outliers start: 29 outliers final: 22 residues processed: 149 average time/residue: 0.1708 time to fit residues: 39.3428 Evaluate side-chains 147 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10331 Z= 0.181 Angle : 0.621 14.082 14005 Z= 0.305 Chirality : 0.042 0.237 1579 Planarity : 0.004 0.048 1804 Dihedral : 5.455 94.804 1396 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 2.53 % Allowed : 27.53 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.25), residues: 1279 helix: 2.07 (0.23), residues: 547 sheet: -0.68 (0.45), residues: 148 loop : -0.77 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 79 HIS 0.004 0.001 HIS A 199 PHE 0.033 0.001 PHE A 946 TYR 0.014 0.001 TYR A 859 ARG 0.002 0.000 ARG A 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 CYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 568 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5900 (m-80) REVERT: A 569 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7254 (p) REVERT: A 754 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: A 842 MET cc_start: 0.9115 (mmm) cc_final: 0.8863 (tpt) REVERT: A 878 LEU cc_start: 0.8330 (mt) cc_final: 0.8084 (mp) REVERT: B 87 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: B 99 GLU cc_start: 0.7770 (tp30) cc_final: 0.7540 (tp30) outliers start: 28 outliers final: 20 residues processed: 150 average time/residue: 0.1745 time to fit residues: 40.4973 Evaluate side-chains 145 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088295 restraints weight = 22515.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090829 restraints weight = 12131.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.092563 restraints weight = 8135.632| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10331 Z= 0.191 Angle : 0.625 13.759 14005 Z= 0.308 Chirality : 0.043 0.236 1579 Planarity : 0.004 0.048 1804 Dihedral : 5.205 74.981 1396 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 2.98 % Allowed : 26.99 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.72 (0.25), residues: 1279 helix: 2.13 (0.23), residues: 547 sheet: -0.79 (0.45), residues: 150 loop : -0.78 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 79 HIS 0.004 0.001 HIS A 199 PHE 0.031 0.001 PHE A 946 TYR 0.014 0.001 TYR A 859 ARG 0.002 0.000 ARG A 901 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.11 seconds wall clock time: 38 minutes 38.66 seconds (2318.66 seconds total)