Starting phenix.real_space_refine on Sun Dec 29 21:12:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwf_18694/12_2024/8qwf_18694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwf_18694/12_2024/8qwf_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_18694/12_2024/8qwf_18694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwf_18694/12_2024/8qwf_18694.map" model { file = "/net/cci-nas-00/data/ceres_data/8qwf_18694/12_2024/8qwf_18694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwf_18694/12_2024/8qwf_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-5532/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: 7.22, per 1000 atoms: 0.63 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: 2.93 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: 4.41 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: 5.50 Time building geometry restraints manager: 3.32 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: 2.010 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.430 Find NCS groups from input model: 0.100 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- 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= 0.150 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 *********************** 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 : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2328 time to fit residues: 24.0965 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 : 1.239 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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= 0.344 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 *********************** 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 : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.2126 time to fit residues: 20.5744 Evaluate side-chains 56 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.1980 chunk 34 optimal weight: 30.0000 chunk 93 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11889 Z= 0.229 Angle : 0.524 9.866 16333 Z= 0.285 Chirality : 0.040 0.162 1755 Planarity : 0.003 0.048 1840 Dihedral : 18.519 165.989 2263 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.10 % Allowed : 6.97 % 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: -0.03 (0.25), residues: 1172 helix: 1.17 (0.23), residues: 514 sheet: -0.10 (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 0.012 0.001 PHE A 99 TYR 0.025 0.001 TYR A 628 ARG 0.001 0.000 ARG A 19 *********************** 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 75 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7057 (ptpt) outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 0.2171 time to fit residues: 23.7772 Evaluate side-chains 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.0050 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 overall best weight: 0.7174 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1274 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= 0.178 Angle : 0.511 11.025 16333 Z= 0.278 Chirality : 0.039 0.164 1755 Planarity : 0.003 0.046 1840 Dihedral : 18.466 166.484 2263 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.92 % Allowed : 8.62 % Favored : 90.47 % 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: 1.30 (0.23), residues: 507 sheet: -0.50 (0.48), residues: 126 loop : -1.09 (0.26), residues: 539 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 0.015 0.001 PHE A 508 TYR 0.021 0.001 TYR A 628 ARG 0.001 0.000 ARG A 879 *********************** 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 72 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.7025 (ptpt) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.2078 time to fit residues: 22.3064 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 : 1.165 ------------------------------------------------------------------------------- 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 99 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.005 0.041 11889 Z= 0.297 Angle : 0.555 9.299 16333 Z= 0.300 Chirality : 0.041 0.180 1755 Planarity : 0.003 0.043 1840 Dihedral : 18.576 164.720 2263 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.19 % Allowed : 9.99 % Favored : 88.82 % 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: 1.16 (0.23), residues: 516 sheet: -0.50 (0.48), residues: 126 loop : -1.08 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 578 HIS 0.005 0.001 HIS A1222 PHE 0.015 0.001 PHE A 99 TYR 0.030 0.002 TYR A 628 ARG 0.002 0.000 ARG A 44 *********************** 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 72 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7840 (mmt) outliers start: 13 outliers final: 5 residues processed: 68 average time/residue: 0.2124 time to fit residues: 22.3812 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 : 1.062 ------------------------------------------------------------------------------- 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 1178 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11889 Z= 0.336 Angle : 0.580 9.950 16333 Z= 0.311 Chirality : 0.042 0.191 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.602 162.611 2263 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.10 % Allowed : 10.63 % 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: -0.17 (0.24), residues: 1172 helix: 1.07 (0.23), residues: 514 sheet: -0.56 (0.48), residues: 126 loop : -1.16 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.015 0.001 PHE A 99 TYR 0.031 0.002 TYR A 628 ARG 0.002 0.000 ARG A 879 *********************** 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 72 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7876 (mmt) outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 0.2344 time to fit residues: 25.2558 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 : 1.242 ------------------------------------------------------------------------------- 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 503 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11889 Z= 0.164 Angle : 0.498 10.240 16333 Z= 0.273 Chirality : 0.038 0.168 1755 Planarity : 0.003 0.045 1840 Dihedral : 18.427 164.371 2263 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.92 % Allowed : 11.09 % 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: 0.07 (0.25), residues: 1172 helix: 1.29 (0.23), residues: 511 sheet: -0.52 (0.48), residues: 126 loop : -1.03 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 136 HIS 0.004 0.001 HIS A1222 PHE 0.013 0.001 PHE A 99 TYR 0.021 0.001 TYR A1108 ARG 0.001 0.000 ARG A 19 *********************** 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 71 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7745 (mmt) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.2137 time to fit residues: 23.1950 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 : 1.163 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 75 optimal weight: 0.0870 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11889 Z= 0.362 Angle : 0.598 15.075 16333 Z= 0.317 Chirality : 0.042 0.207 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.607 162.222 2263 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.10 % Allowed : 11.27 % Favored : 87.63 % 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: 1.09 (0.23), residues: 518 sheet: -0.60 (0.48), residues: 126 loop : -1.13 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 578 HIS 0.006 0.001 HIS A1222 PHE 0.015 0.001 PHE A 99 TYR 0.034 0.002 TYR A 628 ARG 0.002 0.000 ARG A 879 *********************** 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 68 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (mmt) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.2188 time to fit residues: 22.6106 Evaluate side-chains 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 111 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 A1170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1829 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= 0.156 Angle : 0.505 14.642 16333 Z= 0.274 Chirality : 0.038 0.169 1755 Planarity : 0.003 0.044 1840 Dihedral : 18.408 164.019 2263 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.01 % Allowed : 11.46 % 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: 0.11 (0.25), residues: 1172 helix: 1.33 (0.23), residues: 510 sheet: -0.49 (0.48), residues: 126 loop : -1.02 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 PHE 0.013 0.001 PHE A 99 TYR 0.023 0.001 TYR A1108 ARG 0.002 0.000 ARG A 19 *********************** 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 71 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7740 (mmt) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.2214 time to fit residues: 24.3085 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 : 0.887 ------------------------------------------------------------------------------- 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 631 LEU 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 117 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 0.0010 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 11889 Z= 0.220 Angle : 0.774 59.199 16333 Z= 0.457 Chirality : 0.040 0.457 1755 Planarity : 0.003 0.044 1840 Dihedral : 18.410 164.019 2263 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.01 % Allowed : 11.37 % Favored : 87.63 % 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: -0.49 (0.48), residues: 126 loop : -1.03 (0.26), residues: 536 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 0.020 0.001 TYR A1108 ARG 0.002 0.000 ARG A 19 ********************** 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 70 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7688 (p0) REVERT: A 1178 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7748 (mmt) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.2126 time to fit residues: 23.7815 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 : 1.117 ------------------------------------------------------------------------------- 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 631 LEU 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 104 optimal weight: 0.0970 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.218449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.178034 restraints weight = 12645.141| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.49 r_work: 0.3575 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 11889 Z= 0.222 Angle : 0.610 24.097 16333 Z= 0.367 Chirality : 0.039 0.345 1755 Planarity : 0.004 0.098 1840 Dihedral : 18.410 164.019 2263 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.82 % Allowed : 11.55 % Favored : 87.63 % 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: -0.49 (0.48), residues: 126 loop : -1.03 (0.26), residues: 536 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 0.020 0.001 TYR A1108 ARG 0.002 0.000 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.23 seconds wall clock time: 37 minutes 46.43 seconds (2266.43 seconds total)