Starting phenix.real_space_refine on Wed May 14 05:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwf_18694/05_2025/8qwf_18694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwf_18694/05_2025/8qwf_18694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qwf_18694/05_2025/8qwf_18694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwf_18694/05_2025/8qwf_18694.map" model { file = "/net/cci-nas-00/data/ceres_data/8qwf_18694/05_2025/8qwf_18694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwf_18694/05_2025/8qwf_18694.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 77 5.49 5 Mg 6 5.21 5 S 18 5.16 5 C 7067 2.51 5 N 1911 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11501 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9895 Classifications: {'peptide': 1186} Link IDs: {'PTRANS': 30, 'TRANS': 1155} Chain breaks: 6 Chain: "C" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 697 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 8, 'rna3p': 24} Chain: "T" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "N" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 322 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.95, per 1000 atoms: 0.60 Number of scatterers: 11501 At special positions: 0 Unit cell: (95.5608, 99.6798, 141.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 77 15.00 Mg 6 11.99 O 2422 8.00 N 1911 7.00 C 7067 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: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 48.3% alpha, 11.0% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 4.404A pdb=" N ASN A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 38 through 67 removed outlier: 3.506A pdb=" N ALA A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 92 through 117 removed outlier: 4.076A pdb=" N PHE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 125 through 131 removed outlier: 4.167A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.831A pdb=" N ASN A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.523A pdb=" N ARG A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 removed outlier: 3.666A pdb=" N LYS A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.666A pdb=" N ILE A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 315 through 331 removed outlier: 3.565A pdb=" N LEU A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.601A pdb=" N LYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 removed outlier: 4.074A pdb=" N THR A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 491 through 510 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 527 through 542 removed outlier: 4.701A pdb=" N GLU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 removed outlier: 3.656A pdb=" N THR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.573A pdb=" N GLU A 583 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 584 " --> pdb=" O ASN A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 633 through 643 Proline residue: A 639 - end of helix Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 674 through 692 Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.640A pdb=" N GLY A 699 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 710 through 722 removed outlier: 4.012A pdb=" N PHE A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.637A pdb=" N SER A 755 " --> pdb=" O LYS A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.103A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 857 through 868 Processing helix chain 'A' and resid 914 through 931 removed outlier: 3.758A pdb=" N LYS A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 930 " --> pdb=" O ASP A 926 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 961 removed outlier: 3.590A pdb=" N LEU A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 998 removed outlier: 3.888A pdb=" N TYR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1072 removed outlier: 3.755A pdb=" N LYS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1130 through 1141 Processing helix chain 'A' and resid 1161 through 1175 Processing helix chain 'A' and resid 1216 through 1237 removed outlier: 3.812A pdb=" N ALA A1220 " --> pdb=" O ASP A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1257 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 4.796A pdb=" N VAL A 791 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 839 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 22 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR A 597 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 564 through 567 removed outlier: 4.796A pdb=" N VAL A 791 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA4, first strand: chain 'A' and resid 622 through 630 removed outlier: 3.622A pdb=" N ILE A 730 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 810 through 811 Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 901 removed outlier: 6.886A pdb=" N LEU A 889 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN A 899 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU A 887 " --> pdb=" O GLN A 899 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 873 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 965 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE A 875 " --> pdb=" O VAL A 965 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLU A 967 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ILE A 877 " --> pdb=" O GLU A 967 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N PHE A1036 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 964 " --> pdb=" O PHE A1036 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL A1038 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N MET A 966 " --> pdb=" O VAL A1038 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 905 Processing sheet with id=AA9, first strand: chain 'A' and resid 1075 through 1079 removed outlier: 4.109A pdb=" N TYR A1084 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A1089 " --> pdb=" O TRP A1103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 4.964A pdb=" N PHE A1202 " --> pdb=" O SER A1192 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 3.06 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: 2850 1.33 - 1.45: 2645 1.45 - 1.57: 6211 1.57 - 1.69: 151 1.69 - 1.81: 32 Bond restraints: 11889 Sorted by residual: bond pdb=" CB GLN A1236 " pdb=" CG GLN A1236 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.63e-01 bond pdb=" C3' DG N -8 " pdb=" C2' DG N -8 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.00e-02 2.50e+03 6.45e-01 bond pdb=" CA ARG A 279 " pdb=" CB ARG A 279 " ideal model delta sigma weight residual 1.522 1.533 -0.010 1.32e-02 5.74e+03 6.15e-01 bond pdb=" CG GLN A1236 " pdb=" CD GLN A1236 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.65e-01 bond pdb=" CB VAL A1000 " pdb=" CG2 VAL A1000 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.57e-01 ... (remaining 11884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 16178 2.04 - 4.09: 137 4.09 - 6.13: 13 6.13 - 8.17: 4 8.17 - 10.22: 1 Bond angle restraints: 16333 Sorted by residual: angle pdb=" C ILE A 502 " pdb=" N MET A 503 " pdb=" CA MET A 503 " ideal model delta sigma weight residual 121.14 114.60 6.54 1.75e+00 3.27e-01 1.40e+01 angle pdb=" CB MET A 503 " pdb=" CG MET A 503 " pdb=" SD MET A 503 " ideal model delta sigma weight residual 112.70 122.92 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N MET A 503 " pdb=" CA MET A 503 " pdb=" CB MET A 503 " ideal model delta sigma weight residual 110.40 115.81 -5.41 1.63e+00 3.76e-01 1.10e+01 angle pdb=" CA MET A 503 " pdb=" CB MET A 503 " pdb=" CG MET A 503 " ideal model delta sigma weight residual 114.10 119.47 -5.37 2.00e+00 2.50e-01 7.20e+00 angle pdb=" CA ARG A 279 " pdb=" C ARG A 279 " pdb=" N GLN A 280 " ideal model delta sigma weight residual 114.76 117.68 -2.92 1.14e+00 7.69e-01 6.58e+00 ... (remaining 16328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 6763 33.78 - 67.56: 346 67.56 - 101.34: 27 101.34 - 135.11: 0 135.11 - 168.89: 1 Dihedral angle restraints: 7137 sinusoidal: 3620 harmonic: 3517 Sorted by residual: dihedral pdb=" CA HIS A 207 " pdb=" C HIS A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DG T -15 " pdb=" C3' DG T -15 " pdb=" O3' DG T -15 " pdb=" P DG T -14 " ideal model delta sinusoidal sigma weight residual -140.00 28.89 -168.89 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" O4' A C -1 " pdb=" C1' A C -1 " pdb=" N9 A C -1 " pdb=" C4 A C -1 " ideal model delta sinusoidal sigma weight residual 70.00 1.19 68.81 1 2.00e+01 2.50e-03 1.53e+01 ... (remaining 7134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1624 0.069 - 0.139: 126 0.139 - 0.208: 4 0.208 - 0.277: 0 0.277 - 0.347: 1 Chirality restraints: 1755 Sorted by residual: chirality pdb=" CB ILE A1191 " pdb=" CA ILE A1191 " pdb=" CG1 ILE A1191 " pdb=" CG2 ILE A1191 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA GLN A 456 " pdb=" N GLN A 456 " pdb=" C GLN A 456 " pdb=" CB GLN A 456 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 143 " pdb=" CA THR A 143 " pdb=" OG1 THR A 143 " pdb=" CG2 THR A 143 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1752 not shown) Planarity restraints: 1840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 869 " -0.042 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO A 870 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 510 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 511 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U C -15 " -0.016 2.00e-02 2.50e+03 9.76e-03 2.14e+00 pdb=" N1 U C -15 " 0.024 2.00e-02 2.50e+03 pdb=" C2 U C -15 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U C -15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U C -15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U C -15 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U C -15 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U C -15 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U C -15 " 0.000 2.00e-02 2.50e+03 ... (remaining 1837 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 92 2.58 - 3.16: 9329 3.16 - 3.74: 18152 3.74 - 4.32: 25425 4.32 - 4.90: 40352 Nonbonded interactions: 93350 Sorted by model distance: nonbonded pdb=" OD2 ASP A 878 " pdb="MG MG A1303 " model vdw 2.004 2.170 nonbonded pdb=" OD1 ASP A 878 " pdb="MG MG A1303 " model vdw 2.046 2.170 nonbonded pdb=" OP2 A C -3 " pdb="MG MG C1401 " model vdw 2.089 2.170 nonbonded pdb=" O LEU A 902 " pdb=" OH TYR A 945 " model vdw 2.100 3.040 nonbonded pdb=" NH2 ARG A1179 " pdb="MG MG A1304 " model vdw 2.149 2.250 ... (remaining 93345 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 0.026 11889 Z= 0.111 Angle : 0.490 10.215 16333 Z= 0.267 Chirality : 0.038 0.347 1755 Planarity : 0.003 0.062 1840 Dihedral : 18.372 168.892 4861 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.01 (0.25), residues: 1172 helix: 1.31 (0.23), residues: 521 sheet: -0.20 (0.53), residues: 111 loop : -1.27 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1252 HIS 0.003 0.001 HIS A1222 PHE 0.015 0.001 PHE A 978 TYR 0.024 0.001 TYR A1108 ARG 0.001 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.14395 ( 471) hydrogen bonds : angle 5.99063 ( 1310) covalent geometry : bond 0.00240 (11889) covalent geometry : angle 0.48990 (16333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2234 time to fit residues: 23.2484 Evaluate side-chains 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 40.0000 chunk 63 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 122 ASN A 241 ASN A1170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.215114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174790 restraints weight = 12739.953| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.59 r_work: 0.3244 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11889 Z= 0.234 Angle : 0.586 6.705 16333 Z= 0.318 Chirality : 0.042 0.202 1755 Planarity : 0.004 0.051 1840 Dihedral : 18.600 166.598 2263 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.55 % Allowed : 5.22 % Favored : 94.23 % 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: -0.14 (0.25), residues: 1172 helix: 1.07 (0.23), residues: 520 sheet: -0.17 (0.51), residues: 109 loop : -1.24 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 136 HIS 0.006 0.001 HIS A 207 PHE 0.014 0.001 PHE A 99 TYR 0.031 0.002 TYR A 628 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 471) hydrogen bonds : angle 4.75211 ( 1310) covalent geometry : bond 0.00545 (11889) covalent geometry : angle 0.58614 (16333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7793 (ptpt) outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.1998 time to fit residues: 19.4925 Evaluate side-chains 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 28 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 167 ASN A1170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.216443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177362 restraints weight = 12882.019| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.44 r_work: 0.3239 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11889 Z= 0.131 Angle : 0.505 9.949 16333 Z= 0.276 Chirality : 0.039 0.162 1755 Planarity : 0.003 0.048 1840 Dihedral : 18.481 166.741 2263 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.01 % Allowed : 6.97 % Favored : 92.03 % 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: 0.06 (0.25), residues: 1172 helix: 1.25 (0.23), residues: 514 sheet: -0.09 (0.51), residues: 109 loop : -1.12 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 PHE 0.012 0.001 PHE A 99 TYR 0.021 0.001 TYR A 628 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 471) hydrogen bonds : angle 4.40565 ( 1310) covalent geometry : bond 0.00292 (11889) covalent geometry : angle 0.50517 (16333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7638 (ptpt) REVERT: A 1078 TYR cc_start: 0.7803 (t80) cc_final: 0.7545 (t80) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.2267 time to fit residues: 24.4413 Evaluate side-chains 65 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 30 optimal weight: 30.0000 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.218244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175455 restraints weight = 12796.014| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.47 r_work: 0.3248 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11889 Z= 0.132 Angle : 0.508 10.832 16333 Z= 0.275 Chirality : 0.038 0.164 1755 Planarity : 0.003 0.045 1840 Dihedral : 18.446 167.045 2263 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.10 % Allowed : 7.97 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1172 helix: 1.34 (0.23), residues: 509 sheet: -0.48 (0.48), residues: 126 loop : -1.06 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 PHE 0.012 0.001 PHE A 99 TYR 0.022 0.001 TYR A 628 ARG 0.001 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 471) hydrogen bonds : angle 4.28355 ( 1310) covalent geometry : bond 0.00296 (11889) covalent geometry : angle 0.50785 (16333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7612 (ptpt) REVERT: A 1078 TYR cc_start: 0.7771 (t80) cc_final: 0.7503 (t80) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.2674 time to fit residues: 29.8433 Evaluate side-chains 65 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.215058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177722 restraints weight = 12699.715| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.48 r_work: 0.3329 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11889 Z= 0.149 Angle : 0.520 11.583 16333 Z= 0.281 Chirality : 0.039 0.166 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.452 166.695 2263 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.28 % Allowed : 9.44 % Favored : 89.28 % 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: 0.12 (0.25), residues: 1172 helix: 1.27 (0.23), residues: 517 sheet: -0.43 (0.48), residues: 126 loop : -0.97 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.013 0.001 PHE A 99 TYR 0.024 0.001 TYR A 628 ARG 0.001 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 471) hydrogen bonds : angle 4.25830 ( 1310) covalent geometry : bond 0.00339 (11889) covalent geometry : angle 0.52046 (16333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8246 (mmt) outliers start: 14 outliers final: 7 residues processed: 70 average time/residue: 0.1942 time to fit residues: 21.8621 Evaluate side-chains 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.215322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.157254 restraints weight = 12839.854| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.05 r_work: 0.3157 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11889 Z= 0.197 Angle : 0.566 14.165 16333 Z= 0.300 Chirality : 0.041 0.172 1755 Planarity : 0.003 0.040 1840 Dihedral : 18.526 165.143 2263 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.37 % Allowed : 10.17 % Favored : 88.45 % 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: 0.02 (0.25), residues: 1172 helix: 1.18 (0.23), residues: 520 sheet: -0.52 (0.48), residues: 126 loop : -1.02 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.014 0.001 PHE A 99 TYR 0.029 0.001 TYR A 628 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 471) hydrogen bonds : angle 4.33284 ( 1310) covalent geometry : bond 0.00462 (11889) covalent geometry : angle 0.56577 (16333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8394 (mmt) outliers start: 15 outliers final: 7 residues processed: 69 average time/residue: 0.2184 time to fit residues: 23.7922 Evaluate side-chains 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 20 optimal weight: 0.0050 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.217089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.174533 restraints weight = 12923.122| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.76 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11889 Z= 0.154 Angle : 0.531 13.479 16333 Z= 0.286 Chirality : 0.039 0.166 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.485 165.050 2263 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.01 % Allowed : 10.82 % Favored : 88.18 % 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: 0.06 (0.25), residues: 1172 helix: 1.24 (0.23), residues: 518 sheet: -0.56 (0.48), residues: 126 loop : -1.01 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.014 0.001 PHE A 99 TYR 0.024 0.001 TYR A 628 ARG 0.001 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 471) hydrogen bonds : angle 4.23227 ( 1310) covalent geometry : bond 0.00354 (11889) covalent geometry : angle 0.53106 (16333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7753 (mmt) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.2111 time to fit residues: 22.0615 Evaluate side-chains 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.214455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161842 restraints weight = 12778.934| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.86 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11889 Z= 0.222 Angle : 0.573 9.615 16333 Z= 0.308 Chirality : 0.042 0.187 1755 Planarity : 0.003 0.040 1840 Dihedral : 18.586 162.922 2263 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.10 % Allowed : 10.91 % Favored : 87.99 % 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: -0.10 (0.25), residues: 1172 helix: 1.12 (0.23), residues: 518 sheet: -0.62 (0.48), residues: 126 loop : -1.10 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.005 0.001 HIS A 207 PHE 0.015 0.001 PHE A 99 TYR 0.031 0.002 TYR A 628 ARG 0.002 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 471) hydrogen bonds : angle 4.38169 ( 1310) covalent geometry : bond 0.00522 (11889) covalent geometry : angle 0.57293 (16333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7913 (mmt) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.2048 time to fit residues: 21.9747 Evaluate side-chains 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.217851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.165679 restraints weight = 12852.850| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.88 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11889 Z= 0.128 Angle : 0.515 13.772 16333 Z= 0.279 Chirality : 0.038 0.168 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.437 164.013 2263 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.01 % Allowed : 11.00 % Favored : 87.99 % 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: 0.09 (0.25), residues: 1172 helix: 1.26 (0.23), residues: 518 sheet: -0.56 (0.48), residues: 126 loop : -0.98 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.013 0.001 PHE A 99 TYR 0.021 0.001 TYR A 628 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 471) hydrogen bonds : angle 4.12887 ( 1310) covalent geometry : bond 0.00286 (11889) covalent geometry : angle 0.51464 (16333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7770 (mmt) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.2099 time to fit residues: 22.1437 Evaluate side-chains 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 93 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.0040 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 122 ASN A1170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.215908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.165267 restraints weight = 12723.048| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.66 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11889 Z= 0.158 Angle : 0.779 59.200 16333 Z= 0.464 Chirality : 0.040 0.470 1755 Planarity : 0.003 0.043 1840 Dihedral : 18.448 164.018 2263 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.92 % Allowed : 11.00 % Favored : 88.08 % 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: 0.11 (0.25), residues: 1172 helix: 1.28 (0.23), residues: 518 sheet: -0.55 (0.48), residues: 126 loop : -0.97 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.013 0.001 PHE A 99 TYR 0.030 0.001 TYR A 296 ARG 0.002 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 471) hydrogen bonds : angle 4.13314 ( 1310) covalent geometry : bond 0.00331 (11889) covalent geometry : angle 0.77912 (16333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7356 (p0) REVERT: A 1178 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7739 (mmt) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 0.2018 time to fit residues: 21.6916 Evaluate side-chains 68 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.216002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176688 restraints weight = 12746.888| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.48 r_work: 0.3343 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 11889 Z= 0.172 Angle : 0.618 23.597 16333 Z= 0.378 Chirality : 0.039 0.355 1755 Planarity : 0.004 0.093 1840 Dihedral : 18.448 164.018 2263 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.92 % Allowed : 11.00 % Favored : 88.08 % 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: 0.11 (0.25), residues: 1172 helix: 1.28 (0.23), residues: 518 sheet: -0.55 (0.48), residues: 126 loop : -0.97 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.013 0.001 PHE A 99 TYR 0.030 0.001 TYR A 296 ARG 0.002 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 471) hydrogen bonds : angle 4.13314 ( 1310) covalent geometry : bond 0.00343 (11889) covalent geometry : angle 0.61763 (16333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.17 seconds wall clock time: 79 minutes 39.01 seconds (4779.01 seconds total)