Starting phenix.real_space_refine on Wed Mar 4 08:24:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkx_48341/03_2026/9mkx_48341.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkx_48341/03_2026/9mkx_48341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkx_48341/03_2026/9mkx_48341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkx_48341/03_2026/9mkx_48341.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkx_48341/03_2026/9mkx_48341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkx_48341/03_2026/9mkx_48341.cif" } resolution = 3.21 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 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 21 5.16 5 C 7340 2.51 5 N 1953 2.21 5 O 2384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11756 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 10547 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 30, 'TRANS': 1245} Chain breaks: 2 Chain: "B" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 656 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 9, 'rna3p': 21} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 2.29, per 1000 atoms: 0.19 Number of scatterers: 11756 At special positions: 0 Unit cell: (103.2, 110.08, 132.44, 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 21 16.00 P 58 15.00 O 2384 8.00 N 1953 7.00 C 7340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 358.5 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2446 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 46.9% alpha, 8.2% beta 18 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 40 through 69 removed outlier: 4.250A pdb=" N ALA A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 removed outlier: 4.006A pdb=" N ASN A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.639A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.821A pdb=" N LYS A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.696A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.537A pdb=" N ASN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.526A pdb=" N ASP A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.702A pdb=" N LYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.509A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.600A pdb=" N THR A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.207A pdb=" N LYS A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 480 through 499 Proline residue: A 486 - end of helix removed outlier: 3.559A pdb=" N GLN A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.530A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 538 Processing helix chain 'A' and resid 564 through 572 removed outlier: 3.503A pdb=" N CYS A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 588 removed outlier: 3.782A pdb=" N LYS A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 642 through 648 Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.799A pdb=" N VAL A 672 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 713 through 716 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.987A pdb=" N ILE A 721 " --> pdb=" O CYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 743 through 747 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.962A pdb=" N PHE A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 790 through 794 removed outlier: 3.794A pdb=" N PHE A 793 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 794 " --> pdb=" O LYS A 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 790 through 794' Processing helix chain 'A' and resid 802 through 810 Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.819A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 905 removed outlier: 3.603A pdb=" N LYS A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 Processing helix chain 'A' and resid 975 through 998 removed outlier: 4.135A pdb=" N GLU A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1035 removed outlier: 3.789A pdb=" N GLU A1028 " --> pdb=" O TYR A1024 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A1029 " --> pdb=" O GLN A1025 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1112 removed outlier: 4.169A pdb=" N PHE A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1134 removed outlier: 4.176A pdb=" N GLY A1134 " --> pdb=" O TYR A1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1130 through 1134' Processing helix chain 'A' and resid 1169 through 1173 Processing helix chain 'A' and resid 1174 through 1181 Processing helix chain 'A' and resid 1191 through 1198 Processing helix chain 'A' and resid 1200 through 1213 Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 4.001A pdb=" N ALA A1246 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1275 removed outlier: 3.720A pdb=" N ALA A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1298 Processing sheet with id=AA1, first strand: chain 'A' and resid 595 through 597 removed outlier: 4.386A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 21 " --> pdb=" O PHE A 878 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 15 " --> pdb=" O ILE A 884 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 11.837A pdb=" N ALA A 619 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N TYR A 659 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 623 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA4, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AA5, first strand: chain 'A' and resid 935 through 940 removed outlier: 6.832A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN A 938 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR A 926 " --> pdb=" O GLN A 938 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 916 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU A1006 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A1077 " --> pdb=" O PHE A1005 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 943 through 944 Processing sheet with id=AA7, first strand: chain 'A' and resid 1125 through 1129 removed outlier: 4.192A pdb=" N PHE A1126 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1144 " --> pdb=" O PHE A1126 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3165 1.33 - 1.45: 2412 1.45 - 1.57: 6389 1.57 - 1.69: 113 1.69 - 1.81: 33 Bond restraints: 12112 Sorted by residual: bond pdb=" C1' DT C -15 " pdb=" N1 DT C -15 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.81e+00 bond pdb=" N1 DT C -15 " pdb=" C2 DT C -15 " ideal model delta sigma weight residual 1.379 1.401 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C3' DC C -5 " pdb=" C2' DC C -5 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.89e-01 bond pdb=" C3' DA D -1 " pdb=" C2' DA D -1 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.08e-01 bond pdb=" C3' DT C -8 " pdb=" C2' DT C -8 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.00e-02 2.50e+03 6.35e-01 ... (remaining 12107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 16057 1.28 - 2.56: 415 2.56 - 3.84: 55 3.84 - 5.13: 12 5.13 - 6.41: 1 Bond angle restraints: 16540 Sorted by residual: angle pdb=" C2' U B 9 " pdb=" C1' U B 9 " pdb=" N1 U B 9 " ideal model delta sigma weight residual 112.00 116.45 -4.45 1.50e+00 4.44e-01 8.78e+00 angle pdb=" C2' DT C -15 " pdb=" C1' DT C -15 " pdb=" N1 DT C -15 " ideal model delta sigma weight residual 113.50 117.64 -4.14 1.50e+00 4.44e-01 7.60e+00 angle pdb=" C PHE A 879 " pdb=" N PHE A 880 " pdb=" CA PHE A 880 " ideal model delta sigma weight residual 121.85 117.25 4.60 1.77e+00 3.19e-01 6.75e+00 angle pdb=" C LYS A1021 " pdb=" N GLN A1022 " pdb=" CA GLN A1022 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.71e+00 angle pdb=" N SER A1146 " pdb=" CA SER A1146 " pdb=" C SER A1146 " ideal model delta sigma weight residual 110.68 107.21 3.47 1.39e+00 5.18e-01 6.22e+00 ... (remaining 16535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6360 17.93 - 35.87: 709 35.87 - 53.80: 158 53.80 - 71.73: 85 71.73 - 89.66: 17 Dihedral angle restraints: 7329 sinusoidal: 3543 harmonic: 3786 Sorted by residual: dihedral pdb=" CA ILE A 65 " pdb=" C ILE A 65 " pdb=" N LEU A 66 " pdb=" CA LEU A 66 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLN A1022 " pdb=" C GLN A1022 " pdb=" N VAL A1023 " pdb=" CA VAL A1023 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG A 948 " pdb=" CD ARG A 948 " pdb=" NE ARG A 948 " pdb=" CZ ARG A 948 " ideal model delta sinusoidal sigma weight residual -90.00 -133.97 43.97 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 7326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1416 0.045 - 0.090: 316 0.090 - 0.135: 62 0.135 - 0.180: 2 0.180 - 0.225: 1 Chirality restraints: 1797 Sorted by residual: chirality pdb=" C1' U B 9 " pdb=" O4' U B 9 " pdb=" C2' U B 9 " pdb=" N1 U B 9 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" C1' G B 0 " pdb=" O4' G B 0 " pdb=" C2' G B 0 " pdb=" N9 G B 0 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1794 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 683 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO A 684 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 9 " -0.025 2.00e-02 2.50e+03 1.45e-02 4.74e+00 pdb=" N1 U B 9 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 9 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U B 9 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B 9 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U B 9 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U B 9 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 9 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 0 " -0.019 2.00e-02 2.50e+03 8.85e-03 2.35e+00 pdb=" N9 G B 0 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G B 0 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 0 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 0 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 0 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G B 0 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G B 0 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 0 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 0 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 0 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G B 0 " 0.002 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 394 2.71 - 3.26: 11942 3.26 - 3.80: 18374 3.80 - 4.35: 23493 4.35 - 4.90: 37364 Nonbonded interactions: 91567 Sorted by model distance: nonbonded pdb=" OD1 ASN A1153 " pdb=" OG1 THR A1213 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR A 506 " pdb=" OD2 ASP A 522 " model vdw 2.197 3.040 nonbonded pdb=" NH2 ARG A 918 " pdb=" O VAL A1019 " model vdw 2.247 3.120 nonbonded pdb=" ND2 ASN A 851 " pdb=" O LYS A 858 " model vdw 2.280 3.120 nonbonded pdb=" OE2 GLU A 920 " pdb=" NH2 ARG A1218 " model vdw 2.286 3.120 ... (remaining 91562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.002 0.059 12112 Z= 0.113 Angle : 0.498 6.408 16540 Z= 0.290 Chirality : 0.038 0.225 1797 Planarity : 0.003 0.059 1918 Dihedral : 16.823 89.663 4883 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1270 helix: 0.78 (0.24), residues: 503 sheet: -1.56 (0.51), residues: 96 loop : -1.52 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 872 TYR 0.012 0.001 TYR A 579 PHE 0.018 0.001 PHE A 880 TRP 0.006 0.001 TRP A1142 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd covalent geometry : bond 0.00225 (12112) covalent geometry : angle 0.49808 (16540) hydrogen bonds : bond 0.14214 ( 438) hydrogen bonds : angle 5.93651 ( 1226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8327 (mm) cc_final: 0.8040 (tt) REVERT: A 463 PHE cc_start: 0.8699 (t80) cc_final: 0.8335 (t80) REVERT: A 467 ARG cc_start: 0.8435 (mmm160) cc_final: 0.7999 (mmm160) REVERT: A 538 HIS cc_start: 0.8453 (m90) cc_final: 0.8176 (m-70) REVERT: A 1108 PHE cc_start: 0.6756 (m-10) cc_final: 0.6206 (t80) REVERT: A 1250 MET cc_start: 0.7149 (mmt) cc_final: 0.6791 (mmt) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.1234 time to fit residues: 18.4789 Evaluate side-chains 58 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 274 ASN A 560 HIS A 649 ASN A 787 GLN A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.090842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.066611 restraints weight = 47731.445| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.67 r_work: 0.3410 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12112 Z= 0.248 Angle : 0.638 9.406 16540 Z= 0.350 Chirality : 0.043 0.231 1797 Planarity : 0.004 0.046 1918 Dihedral : 15.368 72.745 2150 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.03 % Allowed : 9.13 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1270 helix: 0.61 (0.23), residues: 524 sheet: -1.51 (0.51), residues: 94 loop : -1.76 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 297 TYR 0.024 0.002 TYR A 659 PHE 0.028 0.002 PHE A 880 TRP 0.018 0.002 TRP A 609 HIS 0.006 0.002 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00562 (12112) covalent geometry : angle 0.63847 (16540) hydrogen bonds : bond 0.05979 ( 438) hydrogen bonds : angle 5.19650 ( 1226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8676 (mm) cc_final: 0.8242 (tt) REVERT: A 404 GLN cc_start: 0.8408 (pp30) cc_final: 0.7916 (tp-100) REVERT: A 463 PHE cc_start: 0.8405 (t80) cc_final: 0.8133 (t80) REVERT: A 538 HIS cc_start: 0.8948 (m90) cc_final: 0.8660 (m90) REVERT: A 1221 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8336 (mmmt) REVERT: A 1226 LEU cc_start: 0.8726 (mt) cc_final: 0.7984 (tt) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.1209 time to fit residues: 11.1058 Evaluate side-chains 50 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 1095 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 40.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.090931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.066992 restraints weight = 47913.832| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.65 r_work: 0.3420 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12112 Z= 0.205 Angle : 0.590 10.793 16540 Z= 0.325 Chirality : 0.042 0.218 1797 Planarity : 0.004 0.038 1918 Dihedral : 15.329 72.698 2148 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.07 % Allowed : 11.28 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1270 helix: 0.63 (0.23), residues: 522 sheet: -1.51 (0.51), residues: 94 loop : -1.81 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.021 0.002 TYR A 659 PHE 0.030 0.002 PHE A 880 TRP 0.014 0.001 TRP A 609 HIS 0.005 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00461 (12112) covalent geometry : angle 0.58988 (16540) hydrogen bonds : bond 0.05322 ( 438) hydrogen bonds : angle 4.99082 ( 1226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8665 (mm) cc_final: 0.8253 (tt) REVERT: A 404 GLN cc_start: 0.8449 (pp30) cc_final: 0.7961 (tp-100) REVERT: A 538 HIS cc_start: 0.8834 (m90) cc_final: 0.8541 (m90) REVERT: A 987 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8235 (mm110) REVERT: A 1221 LYS cc_start: 0.8701 (mmtt) cc_final: 0.7749 (mmtp) outliers start: 24 outliers final: 12 residues processed: 66 average time/residue: 0.1058 time to fit residues: 10.5176 Evaluate side-chains 54 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.090520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.066456 restraints weight = 47944.854| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.74 r_work: 0.3405 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12112 Z= 0.216 Angle : 0.594 10.100 16540 Z= 0.326 Chirality : 0.042 0.212 1797 Planarity : 0.004 0.039 1918 Dihedral : 15.341 72.642 2148 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.24 % Allowed : 13.18 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1270 helix: 0.63 (0.23), residues: 523 sheet: -1.51 (0.52), residues: 94 loop : -1.85 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.022 0.002 TYR A 659 PHE 0.029 0.002 PHE A 880 TRP 0.014 0.001 TRP A 609 HIS 0.006 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00486 (12112) covalent geometry : angle 0.59446 (16540) hydrogen bonds : bond 0.05377 ( 438) hydrogen bonds : angle 5.00144 ( 1226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8677 (mm) cc_final: 0.8267 (tt) REVERT: A 404 GLN cc_start: 0.8444 (pp30) cc_final: 0.7945 (tp-100) REVERT: A 463 PHE cc_start: 0.7730 (t80) cc_final: 0.7462 (t80) REVERT: A 538 HIS cc_start: 0.8838 (m90) cc_final: 0.8559 (m90) REVERT: A 987 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8247 (mm110) REVERT: A 1221 LYS cc_start: 0.8725 (mmtt) cc_final: 0.7789 (mmtp) outliers start: 26 outliers final: 19 residues processed: 68 average time/residue: 0.1017 time to fit residues: 10.5017 Evaluate side-chains 62 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.092129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.068091 restraints weight = 47526.610| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.70 r_work: 0.3449 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12112 Z= 0.127 Angle : 0.518 9.947 16540 Z= 0.286 Chirality : 0.039 0.197 1797 Planarity : 0.003 0.034 1918 Dihedral : 15.180 72.863 2148 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.46 % Allowed : 14.73 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.24), residues: 1270 helix: 0.92 (0.24), residues: 523 sheet: -1.37 (0.52), residues: 94 loop : -1.71 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 474 TYR 0.018 0.001 TYR A 682 PHE 0.025 0.001 PHE A 737 TRP 0.007 0.001 TRP A 609 HIS 0.004 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00276 (12112) covalent geometry : angle 0.51790 (16540) hydrogen bonds : bond 0.04228 ( 438) hydrogen bonds : angle 4.67093 ( 1226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8624 (mm) cc_final: 0.8370 (tp) REVERT: A 242 LEU cc_start: 0.8343 (tp) cc_final: 0.8131 (tt) REVERT: A 404 GLN cc_start: 0.8526 (pp30) cc_final: 0.8063 (tp-100) REVERT: A 467 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7294 (mmm160) REVERT: A 538 HIS cc_start: 0.8807 (m90) cc_final: 0.8480 (m90) REVERT: A 1221 LYS cc_start: 0.8696 (mmtt) cc_final: 0.7716 (mmtp) outliers start: 17 outliers final: 13 residues processed: 59 average time/residue: 0.1121 time to fit residues: 9.8521 Evaluate side-chains 56 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 829 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1171 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 21 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.089102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.065121 restraints weight = 48311.765| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.63 r_work: 0.3371 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12112 Z= 0.300 Angle : 0.680 10.181 16540 Z= 0.370 Chirality : 0.044 0.195 1797 Planarity : 0.004 0.042 1918 Dihedral : 15.446 72.563 2148 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.58 % Allowed : 15.25 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1270 helix: 0.54 (0.23), residues: 522 sheet: -1.55 (0.51), residues: 94 loop : -1.93 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 948 TYR 0.026 0.002 TYR A 659 PHE 0.032 0.002 PHE A 880 TRP 0.017 0.002 TRP A 609 HIS 0.007 0.002 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00677 (12112) covalent geometry : angle 0.67971 (16540) hydrogen bonds : bond 0.06259 ( 438) hydrogen bonds : angle 5.20716 ( 1226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 321 MET cc_start: 0.6194 (mmt) cc_final: 0.5472 (mmt) REVERT: A 626 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 817 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7678 (mt) REVERT: A 987 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8340 (mm110) REVERT: A 1221 LYS cc_start: 0.8715 (mmtt) cc_final: 0.7785 (mmtp) outliers start: 30 outliers final: 18 residues processed: 68 average time/residue: 0.0992 time to fit residues: 10.3112 Evaluate side-chains 64 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 829 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 41 optimal weight: 0.0050 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.091834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.068083 restraints weight = 47711.246| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.65 r_work: 0.3448 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12112 Z= 0.123 Angle : 0.531 10.401 16540 Z= 0.293 Chirality : 0.039 0.184 1797 Planarity : 0.003 0.034 1918 Dihedral : 15.175 72.853 2148 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.29 % Allowed : 16.97 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1270 helix: 0.82 (0.24), residues: 522 sheet: -1.48 (0.51), residues: 94 loop : -1.75 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.017 0.001 TYR A 682 PHE 0.027 0.001 PHE A 737 TRP 0.008 0.001 TRP A 609 HIS 0.004 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00271 (12112) covalent geometry : angle 0.53125 (16540) hydrogen bonds : bond 0.04319 ( 438) hydrogen bonds : angle 4.68078 ( 1226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8633 (mm) cc_final: 0.8283 (tp) REVERT: A 321 MET cc_start: 0.6068 (mmt) cc_final: 0.5385 (mmt) REVERT: A 404 GLN cc_start: 0.8243 (pp30) cc_final: 0.7761 (tp-100) REVERT: A 538 HIS cc_start: 0.8843 (m90) cc_final: 0.8492 (m-70) REVERT: A 949 MET cc_start: 0.8422 (mmt) cc_final: 0.7527 (mmt) REVERT: A 987 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8280 (mm110) REVERT: A 1221 LYS cc_start: 0.8741 (mmtt) cc_final: 0.7772 (mmtp) REVERT: A 1250 MET cc_start: 0.7215 (mmt) cc_final: 0.6778 (mmt) outliers start: 15 outliers final: 13 residues processed: 55 average time/residue: 0.1016 time to fit residues: 8.5869 Evaluate side-chains 56 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 829 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 116 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.091392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.067648 restraints weight = 48128.460| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.68 r_work: 0.3439 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12112 Z= 0.145 Angle : 0.533 10.247 16540 Z= 0.293 Chirality : 0.040 0.172 1797 Planarity : 0.003 0.035 1918 Dihedral : 15.149 72.882 2148 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.38 % Allowed : 17.14 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1270 helix: 0.84 (0.23), residues: 530 sheet: -1.39 (0.52), residues: 94 loop : -1.71 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 948 TYR 0.018 0.001 TYR A 659 PHE 0.026 0.001 PHE A 880 TRP 0.008 0.001 TRP A 609 HIS 0.005 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00322 (12112) covalent geometry : angle 0.53271 (16540) hydrogen bonds : bond 0.04408 ( 438) hydrogen bonds : angle 4.63778 ( 1226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8648 (mm) cc_final: 0.8254 (tt) REVERT: A 321 MET cc_start: 0.5965 (mmt) cc_final: 0.5319 (mmt) REVERT: A 404 GLN cc_start: 0.8356 (pp30) cc_final: 0.7936 (tp-100) REVERT: A 949 MET cc_start: 0.8455 (mmt) cc_final: 0.7574 (mmt) REVERT: A 987 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8262 (mm110) REVERT: A 1221 LYS cc_start: 0.8727 (mmtt) cc_final: 0.7758 (mmtp) REVERT: A 1250 MET cc_start: 0.7220 (mmt) cc_final: 0.6790 (mmt) outliers start: 16 outliers final: 12 residues processed: 56 average time/residue: 0.1073 time to fit residues: 9.2335 Evaluate side-chains 53 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 829 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.090540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.066590 restraints weight = 47544.889| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.67 r_work: 0.3432 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12112 Z= 0.188 Angle : 0.574 10.434 16540 Z= 0.314 Chirality : 0.041 0.163 1797 Planarity : 0.003 0.037 1918 Dihedral : 15.207 72.811 2148 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.46 % Allowed : 17.40 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.24), residues: 1270 helix: 0.74 (0.23), residues: 530 sheet: -1.42 (0.52), residues: 94 loop : -1.79 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 948 TYR 0.021 0.002 TYR A 659 PHE 0.028 0.002 PHE A 880 TRP 0.010 0.001 TRP A 609 HIS 0.006 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00423 (12112) covalent geometry : angle 0.57400 (16540) hydrogen bonds : bond 0.04986 ( 438) hydrogen bonds : angle 4.80777 ( 1226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 321 MET cc_start: 0.6071 (mmt) cc_final: 0.5396 (mmt) REVERT: A 404 GLN cc_start: 0.8400 (pp30) cc_final: 0.7969 (tp-100) REVERT: A 817 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7616 (mt) REVERT: A 949 MET cc_start: 0.8470 (mmt) cc_final: 0.7575 (mmt) REVERT: A 987 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8287 (mm110) REVERT: A 1221 LYS cc_start: 0.8728 (mmtt) cc_final: 0.7781 (mmtp) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.0973 time to fit residues: 8.2672 Evaluate side-chains 56 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 829 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 0.1980 chunk 115 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.089772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.065660 restraints weight = 48051.374| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.67 r_work: 0.3394 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12112 Z= 0.227 Angle : 0.616 10.418 16540 Z= 0.336 Chirality : 0.042 0.158 1797 Planarity : 0.004 0.037 1918 Dihedral : 15.298 72.668 2148 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.64 % Allowed : 17.23 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.23), residues: 1270 helix: 0.60 (0.23), residues: 530 sheet: -1.50 (0.51), residues: 94 loop : -1.87 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.023 0.002 TYR A 659 PHE 0.030 0.002 PHE A 880 TRP 0.013 0.001 TRP A 609 HIS 0.007 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00513 (12112) covalent geometry : angle 0.61550 (16540) hydrogen bonds : bond 0.05498 ( 438) hydrogen bonds : angle 4.98685 ( 1226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8261 (tt) REVERT: A 321 MET cc_start: 0.6096 (mmt) cc_final: 0.5459 (mmt) REVERT: A 404 GLN cc_start: 0.8377 (pp30) cc_final: 0.7968 (tp-100) REVERT: A 817 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7632 (mt) REVERT: A 987 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8310 (mm110) REVERT: A 1221 LYS cc_start: 0.8720 (mmtt) cc_final: 0.7794 (mmtp) outliers start: 19 outliers final: 16 residues processed: 57 average time/residue: 0.1017 time to fit residues: 8.7748 Evaluate side-chains 60 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 429 ASN Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 829 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.090646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.066907 restraints weight = 47799.052| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.67 r_work: 0.3417 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12112 Z= 0.171 Angle : 0.562 10.330 16540 Z= 0.308 Chirality : 0.041 0.149 1797 Planarity : 0.003 0.035 1918 Dihedral : 15.199 72.762 2148 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.46 % Allowed : 17.23 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.24), residues: 1270 helix: 0.68 (0.23), residues: 531 sheet: -1.44 (0.51), residues: 94 loop : -1.81 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 948 TYR 0.020 0.001 TYR A 659 PHE 0.027 0.001 PHE A 880 TRP 0.011 0.001 TRP A 609 HIS 0.006 0.001 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00383 (12112) covalent geometry : angle 0.56171 (16540) hydrogen bonds : bond 0.04835 ( 438) hydrogen bonds : angle 4.81118 ( 1226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3894.38 seconds wall clock time: 67 minutes 6.44 seconds (4026.44 seconds total)