Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 18:47:18 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rj9_4900/01_2021/6rj9_4900.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rj9_4900/01_2021/6rj9_4900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rj9_4900/01_2021/6rj9_4900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rj9_4900/01_2021/6rj9_4900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rj9_4900/01_2021/6rj9_4900.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rj9_4900/01_2021/6rj9_4900.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.010 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 11874 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6820 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 815} Chain breaks: 7 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna3p_pyr': 32, 'rna2p_pur': 3, 'rna3p_pur': 37, 'rna2p_pyr': 6} Link IDs: {'rna3p': 68, 'rna2p': 9} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 7.16, per 1000 atoms: 0.60 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Number of scatterers: 11874 At special positions: 0 Unit cell: (120.904, 141.351, 110.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 97 15.00 O 2505 8.00 N 2050 7.00 C 7185 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 Amimo 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: 5.12 Conformation dependent library (CDL) restraints added in 1.4 seconds 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 45.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.799A pdb=" N LYS A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.987A pdb=" N ASP A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.653A pdb=" N LYS A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 87' Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.773A pdb=" N TYR A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'B' and resid 4 through 19 removed outlier: 4.060A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.685A pdb=" N GLN B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.550A pdb=" N MET B 71 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.554A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.625A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.633A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.934A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.715A pdb=" N HIS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.661A pdb=" N GLU C 147 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 148 " --> pdb=" O GLN C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.890A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 272 through 284 removed outlier: 3.753A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 310 Processing helix chain 'C' and resid 316 through 327 removed outlier: 3.737A pdb=" N PHE C 320 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.927A pdb=" N ALA C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 392 Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.777A pdb=" N PHE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.553A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 454 removed outlier: 3.953A pdb=" N ILE C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 479 through 500 removed outlier: 4.109A pdb=" N LYS C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 485 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 704 removed outlier: 3.636A pdb=" N LEU C 695 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 727 removed outlier: 3.701A pdb=" N THR C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 727 " --> pdb=" O ARG C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 749 removed outlier: 3.955A pdb=" N ASP C 741 " --> pdb=" O HIS C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 868 removed outlier: 4.082A pdb=" N LYS C 867 " --> pdb=" O LYS C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 871 No H-bonds generated for 'chain 'C' and resid 869 through 871' Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.999A pdb=" N ARG C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 886 Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.642A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.650A pdb=" N MET B 121 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 710 through 713 removed outlier: 3.708A pdb=" N HIS C 29 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS C 30 " --> pdb=" O LEU C 809 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N SER C 811 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 32 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 168 through 172 Processing sheet with id=AA6, first strand: chain 'C' and resid 934 through 941 removed outlier: 6.606A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.941A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.941A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 967 " --> pdb=" O THR C1022 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR C1022 " --> pdb=" O ALA C 967 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 969 " --> pdb=" O LYS C1020 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB1, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.305A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1158 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: 5.30 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: 2303 1.33 - 1.45: 3417 1.45 - 1.57: 6314 1.57 - 1.69: 190 1.69 - 1.82: 69 Bond restraints: 12293 Sorted by residual: bond pdb=" C1' DC E 15 " pdb=" N1 DC E 15 " ideal model delta sigma weight residual 1.490 1.538 -0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CB MET A 152 " pdb=" CG MET A 152 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB ILE C 827 " pdb=" CG2 ILE C 827 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 bond pdb=" CB VAL C 957 " pdb=" CG1 VAL C 957 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB ARG A 153 " pdb=" CG ARG A 153 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.64e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.52: 572 105.52 - 112.69: 6287 112.69 - 119.85: 4613 119.85 - 127.01: 5204 127.01 - 134.18: 290 Bond angle restraints: 16966 Sorted by residual: angle pdb=" CA LEU C 439 " pdb=" CB LEU C 439 " pdb=" CG LEU C 439 " ideal model delta sigma weight residual 116.30 128.70 -12.40 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C ASN C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.50e+00 angle pdb=" CA TYR A 26 " pdb=" CB TYR A 26 " pdb=" CG TYR A 26 " ideal model delta sigma weight residual 113.90 118.91 -5.01 1.80e+00 3.09e-01 7.74e+00 angle pdb=" CA TYR B 26 " pdb=" CB TYR B 26 " pdb=" CG TYR B 26 " ideal model delta sigma weight residual 113.90 118.67 -4.77 1.80e+00 3.09e-01 7.03e+00 angle pdb=" CA GLU C 887 " pdb=" C GLU C 887 " pdb=" N PRO C 888 " ideal model delta sigma weight residual 118.44 122.65 -4.21 1.59e+00 3.96e-01 7.01e+00 ... (remaining 16961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6275 17.92 - 35.83: 761 35.83 - 53.75: 133 53.75 - 71.66: 31 71.66 - 89.58: 9 Dihedral angle restraints: 7209 sinusoidal: 3700 harmonic: 3509 Sorted by residual: dihedral pdb=" CA GLU C 991 " pdb=" C GLU C 991 " pdb=" N LYS C 992 " pdb=" CA LYS C 992 " ideal model delta harmonic sigma weight residual 180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU C 439 " pdb=" C LEU C 439 " pdb=" N TYR C 440 " pdb=" CA TYR C 440 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR C1036 " pdb=" C THR C1036 " pdb=" N LYS C1037 " pdb=" CA LYS C1037 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 7206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1119 0.036 - 0.071: 550 0.071 - 0.107: 152 0.107 - 0.142: 67 0.142 - 0.178: 4 Chirality restraints: 1892 Sorted by residual: chirality pdb=" CB ILE B 164 " pdb=" CA ILE B 164 " pdb=" CG1 ILE B 164 " pdb=" CG2 ILE B 164 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE C 946 " pdb=" N ILE C 946 " pdb=" C ILE C 946 " pdb=" CB ILE C 946 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1889 not shown) Planarity restraints: 1823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 375 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU C 375 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU C 375 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 376 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 376 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C ALA C 376 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA C 376 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR C 377 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 881 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C THR C 881 " 0.048 2.00e-02 2.50e+03 pdb=" O THR C 881 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE C 882 " -0.016 2.00e-02 2.50e+03 ... (remaining 1820 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3387 2.81 - 3.34: 9264 3.34 - 3.86: 19203 3.86 - 4.38: 22824 4.38 - 4.90: 38223 Nonbonded interactions: 92901 Sorted by model distance: nonbonded pdb=" O ILE C 84 " pdb=" O2' A D 63 " model vdw 2.292 2.440 nonbonded pdb=" OD2 ASP C 968 " pdb=" OH TYR C1004 " model vdw 2.330 2.440 nonbonded pdb=" OG1 THR C1034 " pdb=" O ASN C1093 " model vdw 2.335 2.440 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.336 2.440 nonbonded pdb=" O SER C 101 " pdb=" OG SER C 101 " model vdw 2.345 2.440 ... (remaining 92896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 3012 11874 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 37 5.16 5 C 7185 2.51 5 N 2050 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 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: 0.990 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.060 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.060 Process input model: 35.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.890 Internal consistency checks: 0.000 Total: 46.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.053 12293 Angle : 0.783 12.396 16966 Chirality : 0.046 0.178 1892 Planarity : 0.006 0.055 1823 Dihedral : 15.209 89.577 4961 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 0.28 % 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: -3.87 (0.19), residues: 1182 helix: -2.59 (0.17), residues: 493 sheet: -0.93 (0.45), residues: 122 loop : -2.91 (0.19), residues: 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.457 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 195 average time/residue: 0.2737 time to fit residues: 55.6010 Evaluate side-chains 158 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1226 time to fit residues: 1.9555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 43 ASN A 161 GLN B 177 ASN C 43 ASN C 85 ASN C 87 ASN C 115 HIS C 276 GLN C 282 ASN C 303 GLN ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 ASN C 880 GLN C1039 GLN C1093 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.033 12293 Angle : 0.436 8.606 16966 Chirality : 0.034 0.133 1892 Planarity : 0.003 0.038 1823 Dihedral : 9.328 68.547 2439 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.00 % 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: -2.11 (0.22), residues: 1182 helix: -0.47 (0.22), residues: 491 sheet: -0.47 (0.44), residues: 136 loop : -2.57 (0.21), residues: 555 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.586 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2835 time to fit residues: 58.5261 Evaluate side-chains 155 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 181 ASN B 43 ASN B 178 ASN C 29 HIS ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.031 12293 Angle : 0.517 7.468 16966 Chirality : 0.038 0.139 1892 Planarity : 0.004 0.050 1823 Dihedral : 9.672 68.658 2439 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 0.00 % 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: -1.48 (0.23), residues: 1182 helix: 0.31 (0.23), residues: 496 sheet: -0.63 (0.42), residues: 147 loop : -2.39 (0.22), residues: 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.424 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2569 time to fit residues: 47.5228 Evaluate side-chains 153 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN C 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.033 12293 Angle : 0.418 9.055 16966 Chirality : 0.034 0.133 1892 Planarity : 0.003 0.068 1823 Dihedral : 9.050 68.532 2439 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.00 % 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: -0.96 (0.24), residues: 1182 helix: 0.86 (0.24), residues: 493 sheet: -0.39 (0.43), residues: 153 loop : -2.23 (0.23), residues: 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.483 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2522 time to fit residues: 50.4109 Evaluate side-chains 165 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 1 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 30 optimal weight: 0.0070 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 181 ASN B 81 ASN B 151 GLN C 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.026 12293 Angle : 0.400 9.145 16966 Chirality : 0.034 0.137 1892 Planarity : 0.003 0.065 1823 Dihedral : 8.704 68.257 2439 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.00 % 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: -0.56 (0.24), residues: 1182 helix: 1.25 (0.24), residues: 495 sheet: -0.29 (0.43), residues: 153 loop : -2.04 (0.23), residues: 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2466 time to fit residues: 50.9103 Evaluate side-chains 165 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.1980 chunk 122 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 178 ASN C 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.050 12293 Angle : 0.527 8.060 16966 Chirality : 0.039 0.165 1892 Planarity : 0.004 0.084 1823 Dihedral : 9.412 68.188 2439 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.00 % 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: -0.72 (0.24), residues: 1182 helix: 1.05 (0.24), residues: 495 sheet: -0.28 (0.43), residues: 153 loop : -2.09 (0.23), residues: 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.516 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2617 time to fit residues: 48.5417 Evaluate side-chains 154 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 HIS C 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.033 12293 Angle : 0.531 8.961 16966 Chirality : 0.039 0.183 1892 Planarity : 0.004 0.075 1823 Dihedral : 9.553 68.180 2439 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.09 % 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: -0.66 (0.24), residues: 1182 helix: 1.11 (0.24), residues: 488 sheet: -0.41 (0.44), residues: 147 loop : -1.96 (0.23), residues: 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.578 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.2515 time to fit residues: 46.2619 Evaluate side-chains 153 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1259 time to fit residues: 1.9659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 96 optimal weight: 0.0670 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 29 HIS C 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.087 12293 Angle : 0.522 8.306 16966 Chirality : 0.039 0.150 1892 Planarity : 0.004 0.099 1823 Dihedral : 9.546 68.175 2439 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1182 helix: 1.07 (0.24), residues: 492 sheet: -0.29 (0.44), residues: 153 loop : -2.01 (0.23), residues: 537 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.393 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2451 time to fit residues: 45.4117 Evaluate side-chains 156 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.113 12293 Angle : 0.442 9.076 16966 Chirality : 0.035 0.194 1892 Planarity : 0.004 0.114 1823 Dihedral : 9.043 68.531 2439 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.00 % 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: -0.41 (0.24), residues: 1182 helix: 1.35 (0.24), residues: 496 sheet: -0.26 (0.43), residues: 153 loop : -1.93 (0.24), residues: 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.383 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2557 time to fit residues: 47.2388 Evaluate side-chains 154 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.175 12293 Angle : 0.550 17.745 16966 Chirality : 0.039 0.203 1892 Planarity : 0.005 0.133 1823 Dihedral : 9.410 67.748 2439 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.00 % 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: -0.48 (0.24), residues: 1182 helix: 1.30 (0.24), residues: 488 sheet: -0.38 (0.43), residues: 153 loop : -1.88 (0.24), residues: 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield and 0 Emsley and 1182 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2523 time to fit residues: 45.1782 Evaluate side-chains 150 residues out of total 1063 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 0.0770 chunk 30 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.163985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131745 restraints weight = 16013.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133005 restraints weight = 16279.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134754 restraints weight = 10017.832| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.029 12293 ANGLE : 0.438 8.592 16966 CHIRALITY : 0.035 0.179 1892 PLANARITY : 0.003 0.035 1823 DIHEDRAL : 8.988 68.446 2439 MIN NONBONDED DISTANCE : 2.238 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.05 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.15 % FAVORED : 95.85 % ROTAMER OUTLIERS : 0.00 % 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: -0.26 (0.24), RESIDUES: 1182 HELIX: 1.54 (0.24), RESIDUES: 491 SHEET: -0.26 (0.43), RESIDUES: 152 LOOP : -1.85 (0.24), RESIDUES: 539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.029 12293 Angle : 0.438 8.592 16966 Chirality : 0.035 0.179 1892 Planarity : 0.003 0.035 1823 Dihedral : 8.988 68.446 2439 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.00 % 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: -0.26 (0.24), residues: 1182 helix: 1.54 (0.24), residues: 491 sheet: -0.26 (0.43), residues: 152 loop : -1.85 (0.24), residues: 539 =============================================================================== Job complete usr+sys time: 2158.80 seconds wall clock time: 40 minutes 37.80 seconds (2437.80 seconds total)