Starting phenix.real_space_refine on Tue Jul 29 14:23:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwf_18694/07_2025/8qwf_18694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwf_18694/07_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_18694/07_2025/8qwf_18694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwf_18694/07_2025/8qwf_18694.map" model { file = "/net/cci-nas-00/data/ceres_data/8qwf_18694/07_2025/8qwf_18694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwf_18694/07_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-5711/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: 7.51, per 1000 atoms: 0.65 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 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: 3.77 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: 4.86 Time building geometry restraints manager: 3.42 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.230 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- 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 : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2225 time to fit residues: 23.1966 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 : 1.234 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.212963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178824 restraints weight = 12691.354| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.30 r_work: 0.3337 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1086 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= 0.231 Angle : 0.585 6.674 16333 Z= 0.318 Chirality : 0.042 0.204 1755 Planarity : 0.004 0.051 1840 Dihedral : 18.597 166.650 2263 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.55 % Allowed : 5.13 % Favored : 94.32 % 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 0.011 0.001 TRP A 136 HIS 0.006 0.001 HIS A 207 PHE 0.014 0.001 PHE A1094 TYR 0.031 0.002 TYR A 628 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 471) hydrogen bonds : angle 4.75455 ( 1310) covalent geometry : bond 0.00541 (11889) covalent geometry : angle 0.58547 (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 : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7698 (ptpt) outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 0.2061 time to fit residues: 20.2710 Evaluate side-chains 55 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.0070 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 28 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.215079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168449 restraints weight = 12872.192| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.55 r_work: 0.3277 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11889 Z= 0.163 Angle : 0.526 9.628 16333 Z= 0.286 Chirality : 0.040 0.162 1755 Planarity : 0.003 0.048 1840 Dihedral : 18.523 165.824 2263 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.01 % Allowed : 7.06 % Favored : 91.93 % 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: -0.04 (0.25), residues: 1172 helix: 1.16 (0.23), residues: 514 sheet: -0.12 (0.51), residues: 109 loop : -1.16 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 PHE 0.013 0.001 PHE A 99 TYR 0.025 0.001 TYR A 628 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 471) hydrogen bonds : angle 4.47311 ( 1310) covalent geometry : bond 0.00376 (11889) covalent geometry : angle 0.52598 (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 73 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7710 (ptpt) REVERT: A 1078 TYR cc_start: 0.7855 (t80) cc_final: 0.7549 (t80) outliers start: 11 outliers final: 5 residues processed: 69 average time/residue: 0.2203 time to fit residues: 24.0272 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 : 1.143 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.216003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160385 restraints weight = 12764.839| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.10 r_work: 0.3203 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1307 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= 0.137 Angle : 0.518 10.907 16333 Z= 0.281 Chirality : 0.039 0.164 1755 Planarity : 0.003 0.046 1840 Dihedral : 18.483 166.144 2263 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.73 % Allowed : 8.89 % Favored : 90.38 % 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: 0.03 (0.25), residues: 1172 helix: 1.24 (0.23), residues: 513 sheet: -0.52 (0.48), residues: 126 loop : -1.05 (0.26), residues: 533 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 0.014 0.001 PHE A 508 TYR 0.023 0.001 TYR A 628 ARG 0.001 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 471) hydrogen bonds : angle 4.34296 ( 1310) covalent geometry : bond 0.00309 (11889) covalent geometry : angle 0.51767 (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 69 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7619 (ptpt) REVERT: A 1078 TYR cc_start: 0.7911 (t80) cc_final: 0.7608 (t80) REVERT: A 1178 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8274 (mmt) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.1999 time to fit residues: 21.8063 Evaluate side-chains 63 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS 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: 0.7980 chunk 29 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.216469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163710 restraints weight = 12726.627| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.81 r_work: 0.3141 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11889 Z= 0.158 Angle : 0.521 9.229 16333 Z= 0.283 Chirality : 0.039 0.166 1755 Planarity : 0.003 0.043 1840 Dihedral : 18.489 165.804 2263 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.19 % Allowed : 9.81 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1172 helix: 1.25 (0.23), residues: 516 sheet: -0.47 (0.48), residues: 126 loop : -1.03 (0.26), residues: 530 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 0.025 0.001 TYR A 628 ARG 0.002 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 471) hydrogen bonds : angle 4.30847 ( 1310) covalent geometry : bond 0.00362 (11889) covalent geometry : angle 0.52114 (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: 13 poor density : 61 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7793 (ptpt) REVERT: A 1178 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8378 (mmt) outliers start: 13 outliers final: 6 residues processed: 71 average time/residue: 0.2818 time to fit residues: 31.5702 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 : 1.229 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 843 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 6.9990 chunk 74 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.0040 chunk 7 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 overall best weight: 1.0054 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.216933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165845 restraints weight = 12835.221| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.64 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11889 Z= 0.150 Angle : 0.522 9.914 16333 Z= 0.282 Chirality : 0.039 0.198 1755 Planarity : 0.003 0.041 1840 Dihedral : 18.467 165.721 2263 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.19 % Allowed : 10.54 % Favored : 88.27 % 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: 0.08 (0.25), residues: 1172 helix: 1.25 (0.23), residues: 516 sheet: -0.50 (0.48), residues: 126 loop : -1.00 (0.27), residues: 530 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 0.03467 ( 471) hydrogen bonds : angle 4.24153 ( 1310) covalent geometry : bond 0.00342 (11889) covalent geometry : angle 0.52223 (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 74 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.1868 (OUTLIER) cc_final: 0.0583 (ptp) REVERT: A 1072 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7272 (ptpt) REVERT: A 1178 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7793 (mmt) outliers start: 13 outliers final: 6 residues processed: 71 average time/residue: 0.2075 time to fit residues: 23.7970 Evaluate side-chains 69 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 503 MET 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=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: 10.0000 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 119 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.209970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173270 restraints weight = 12909.241| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.44 r_work: 0.3139 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 11889 Z= 0.344 Angle : 0.680 14.652 16333 Z= 0.356 Chirality : 0.046 0.252 1755 Planarity : 0.004 0.042 1840 Dihedral : 18.754 160.134 2263 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.28 % Allowed : 11.27 % Favored : 87.44 % 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: -0.34 (0.24), residues: 1172 helix: 0.89 (0.23), residues: 517 sheet: -0.14 (0.51), residues: 109 loop : -1.34 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 578 HIS 0.005 0.002 HIS A 207 PHE 0.017 0.002 PHE A1094 TYR 0.038 0.002 TYR A 628 ARG 0.004 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 471) hydrogen bonds : angle 4.67860 ( 1310) covalent geometry : bond 0.00812 (11889) covalent geometry : angle 0.67964 (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 74 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 503 MET cc_start: 0.2919 (OUTLIER) cc_final: 0.1723 (ptp) outliers start: 14 outliers final: 6 residues processed: 71 average time/residue: 0.2341 time to fit residues: 26.7324 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 : 1.349 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 503 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 20.0000 chunk 117 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 110 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.217389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156117 restraints weight = 12768.974| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.64 r_work: 0.3206 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11889 Z= 0.123 Angle : 0.520 14.100 16333 Z= 0.281 Chirality : 0.038 0.170 1755 Planarity : 0.003 0.044 1840 Dihedral : 18.497 161.293 2263 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.01 % Allowed : 11.55 % Favored : 87.44 % 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: -0.07 (0.25), residues: 1172 helix: 1.12 (0.23), residues: 518 sheet: -0.57 (0.48), residues: 126 loop : -1.07 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 A1108 ARG 0.002 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 471) hydrogen bonds : angle 4.21703 ( 1310) covalent geometry : bond 0.00272 (11889) covalent geometry : angle 0.51985 (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 71 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.3332 (OUTLIER) cc_final: 0.2593 (ptp) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.2601 time to fit residues: 28.7440 Evaluate side-chains 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.214174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.165574 restraints weight = 12834.555| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.71 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11889 Z= 0.226 Angle : 0.583 13.790 16333 Z= 0.311 Chirality : 0.042 0.196 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.602 160.036 2263 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.92 % Allowed : 11.55 % Favored : 87.53 % 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 (0.24), residues: 1172 helix: 1.06 (0.23), residues: 517 sheet: -0.12 (0.51), residues: 109 loop : -1.23 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.015 0.001 PHE A 99 TYR 0.032 0.002 TYR A 628 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 471) hydrogen bonds : angle 4.38372 ( 1310) covalent geometry : bond 0.00531 (11889) covalent geometry : angle 0.58316 (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 68 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 503 MET cc_start: 0.1702 (OUTLIER) cc_final: 0.0623 (ptp) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.3654 time to fit residues: 38.0975 Evaluate side-chains 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 503 MET 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 99 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 93 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 122 ASN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.219651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161324 restraints weight = 12748.381| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.11 r_work: 0.3130 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11889 Z= 0.107 Angle : 0.503 13.581 16333 Z= 0.274 Chirality : 0.038 0.172 1755 Planarity : 0.003 0.043 1840 Dihedral : 18.402 162.252 2263 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.73 % Allowed : 12.01 % Favored : 87.26 % 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: 1.33 (0.23), residues: 510 sheet: -0.52 (0.48), residues: 126 loop : -1.02 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 136 HIS 0.004 0.001 HIS A 207 PHE 0.020 0.001 PHE A 124 TYR 0.024 0.001 TYR A1108 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 471) hydrogen bonds : angle 4.03803 ( 1310) covalent geometry : bond 0.00229 (11889) covalent geometry : angle 0.50288 (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 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 503 MET cc_start: 0.3305 (OUTLIER) cc_final: 0.2486 (ptp) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.2864 time to fit residues: 30.2599 Evaluate side-chains 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL 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: 0.5980 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.216378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162669 restraints weight = 12743.694| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.74 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11889 Z= 0.168 Angle : 0.533 13.250 16333 Z= 0.287 Chirality : 0.040 0.169 1755 Planarity : 0.003 0.045 1840 Dihedral : 18.448 162.415 2263 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.92 % Allowed : 11.92 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.25), residues: 1172 helix: 1.29 (0.23), residues: 511 sheet: -0.54 (0.48), residues: 126 loop : -1.03 (0.27), residues: 535 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 0.016 0.001 PHE A 978 TYR 0.026 0.001 TYR A 628 ARG 0.002 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 471) hydrogen bonds : angle 4.16114 ( 1310) covalent geometry : bond 0.00387 (11889) covalent geometry : angle 0.53327 (16333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5738.22 seconds wall clock time: 105 minutes 39.23 seconds (6339.23 seconds total)