Starting phenix.real_space_refine on Fri Jul 3 12:12:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s36_24817/07_2026/7s36_24817.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.091 sd= 1.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 130 5.49 5 S 25 5.16 5 C 8311 2.51 5 N 2413 2.21 5 O 2942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13821 Number of models: 1 Model: "" Number of chains: 5 Chain: "N" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 458 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "P" Number of atoms: 11065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 11065 Classifications: {'peptide': 1353} Link IDs: {'PTRANS': 35, 'TRANS': 1317} Chain breaks: 1 Chain: "R" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1854 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 41, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 74} Chain: "T" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 101 Classifications: {'DNA': 5} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 4} Chain: "T" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 343 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.59, per 1000 atoms: 0.26 Number of scatterers: 13821 At special positions: 0 Unit cell: (123.9, 114.45, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 130 15.00 O 2942 8.00 N 2413 7.00 C 8311 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 619.7 milliseconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2574 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 9 sheets defined 54.8% alpha, 7.8% beta 42 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'P' and resid 59 through 94 removed outlier: 5.209A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 Processing helix chain 'P' and resid 121 through 132 Processing helix chain 'P' and resid 134 through 145 removed outlier: 3.802A pdb=" N LEU P 138 " --> pdb=" O THR P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 Processing helix chain 'P' and resid 180 through 196 Processing helix chain 'P' and resid 207 through 213 Processing helix chain 'P' and resid 217 through 228 removed outlier: 3.578A pdb=" N GLN P 228 " --> pdb=" O ASN P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 247 Processing helix chain 'P' and resid 252 through 257 removed outlier: 3.503A pdb=" N PHE P 256 " --> pdb=" O PHE P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 283 removed outlier: 3.521A pdb=" N ASP P 274 " --> pdb=" O THR P 270 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 306 Processing helix chain 'P' and resid 315 through 343 Processing helix chain 'P' and resid 346 through 352 removed outlier: 3.619A pdb=" N ILE P 350 " --> pdb=" O LYS P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 358 through 364 Processing helix chain 'P' and resid 368 through 383 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 389 through 395 Processing helix chain 'P' and resid 404 through 410 removed outlier: 3.766A pdb=" N GLY P 408 " --> pdb=" O PHE P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 426 removed outlier: 4.152A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 436 removed outlier: 3.705A pdb=" N LYS P 434 " --> pdb=" O TYR P 430 " (cutoff:3.500A) Processing helix chain 'P' and resid 436 through 446 Processing helix chain 'P' and resid 477 through 482 Processing helix chain 'P' and resid 483 through 496 Processing helix chain 'P' and resid 512 through 525 Processing helix chain 'P' and resid 541 through 552 Processing helix chain 'P' and resid 560 through 568 Processing helix chain 'P' and resid 591 through 602 Processing helix chain 'P' and resid 603 through 608 removed outlier: 3.549A pdb=" N LEU P 607 " --> pdb=" O ASP P 603 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP P 608 " --> pdb=" O LYS P 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 603 through 608' Processing helix chain 'P' and resid 609 through 611 No H-bonds generated for 'chain 'P' and resid 609 through 611' Processing helix chain 'P' and resid 612 through 626 Processing helix chain 'P' and resid 628 through 636 Processing helix chain 'P' and resid 646 through 654 removed outlier: 3.670A pdb=" N GLN P 650 " --> pdb=" O LYS P 646 " (cutoff:3.500A) Processing helix chain 'P' and resid 664 through 669 Processing helix chain 'P' and resid 678 through 685 Processing helix chain 'P' and resid 692 through 699 Processing helix chain 'P' and resid 703 through 711 Processing helix chain 'P' and resid 711 through 716 removed outlier: 3.610A pdb=" N GLY P 715 " --> pdb=" O ALA P 711 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN P 716 " --> pdb=" O GLN P 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 711 through 716' Processing helix chain 'P' and resid 719 through 726 Processing helix chain 'P' and resid 730 through 751 Processing helix chain 'P' and resid 775 through 792 Processing helix chain 'P' and resid 794 through 799 removed outlier: 3.588A pdb=" N GLU P 798 " --> pdb=" O GLN P 794 " (cutoff:3.500A) Processing helix chain 'P' and resid 804 through 807 removed outlier: 3.661A pdb=" N GLN P 807 " --> pdb=" O THR P 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 804 through 807' Processing helix chain 'P' and resid 808 through 817 Processing helix chain 'P' and resid 851 through 853 No H-bonds generated for 'chain 'P' and resid 851 through 853' Processing helix chain 'P' and resid 860 through 865 removed outlier: 3.530A pdb=" N ASN P 863 " --> pdb=" O SER P 860 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) Processing helix chain 'P' and resid 872 through 889 removed outlier: 3.790A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR P 882 " --> pdb=" O LYS P 878 " (cutoff:3.500A) Processing helix chain 'P' and resid 893 through 901 Processing helix chain 'P' and resid 902 through 906 Processing helix chain 'P' and resid 909 through 922 Processing helix chain 'P' and resid 925 through 940 removed outlier: 3.585A pdb=" N LYS P 929 " --> pdb=" O ARG P 925 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 970 removed outlier: 3.987A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 980 through 1001 removed outlier: 4.515A pdb=" N ALA P 984 " --> pdb=" O ASN P 980 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 3.797A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1017 through 1022 removed outlier: 4.255A pdb=" N MET P1021 " --> pdb=" O ASP P1017 " (cutoff:3.500A) Processing helix chain 'P' and resid 1041 through 1045 removed outlier: 3.647A pdb=" N ASN P1044 " --> pdb=" O ASN P1041 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE P1045 " --> pdb=" O ILE P1042 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1041 through 1045' Processing helix chain 'P' and resid 1077 through 1089 Processing helix chain 'P' and resid 1127 through 1132 Processing helix chain 'P' and resid 1170 through 1177 Processing helix chain 'P' and resid 1177 through 1186 Processing helix chain 'P' and resid 1191 through 1195 Processing helix chain 'P' and resid 1207 through 1209 No H-bonds generated for 'chain 'P' and resid 1207 through 1209' Processing helix chain 'P' and resid 1229 through 1241 Processing helix chain 'P' and resid 1248 through 1262 Processing helix chain 'P' and resid 1264 through 1280 Processing helix chain 'P' and resid 1283 through 1297 Processing helix chain 'P' and resid 1301 through 1313 removed outlier: 3.623A pdb=" N HIS P1311 " --> pdb=" O GLU P1307 " (cutoff:3.500A) Processing helix chain 'P' and resid 1314 through 1316 No H-bonds generated for 'chain 'P' and resid 1314 through 1316' Processing helix chain 'P' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'P' and resid 954 through 957 removed outlier: 6.531A pdb=" N ILE P 7 " --> pdb=" O VAL P 760 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLU P 762 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU P 9 " --> pdb=" O GLU P 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 42 through 46 removed outlier: 9.835A pdb=" N GLU P1357 " --> pdb=" O LYS P 31 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS P 33 " --> pdb=" O GLU P1357 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ARG P1359 " --> pdb=" O LYS P 33 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU P 35 " --> pdb=" O ARG P1359 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP P1361 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 507 through 509 removed outlier: 5.974A pdb=" N LEU P 508 " --> pdb=" O GLY P 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 538 through 539 removed outlier: 3.557A pdb=" N GLU P 579 " --> pdb=" O VAL P 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'P' and resid 1049 through 1051 Processing sheet with id=AA7, first strand: chain 'P' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'P' and resid 1157 through 1167 removed outlier: 3.563A pdb=" N TYR P1141 " --> pdb=" O ILE P1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 1324 through 1326 508 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2198 1.32 - 1.45: 4299 1.45 - 1.57: 7531 1.57 - 1.69: 271 1.69 - 1.81: 46 Bond restraints: 14345 Sorted by residual: bond pdb=" O5' 2YR T 6 " pdb=" P 2YR T 6 " ideal model delta sigma weight residual 1.721 1.597 0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C1' DC N 30 " pdb=" N1 DC N 30 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" C1' DT T 22 " pdb=" N1 DT T 22 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" C1' DC T 20 " pdb=" N1 DC T 20 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" C1' DC T 15 " pdb=" N1 DC T 15 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.64e+01 ... (remaining 14340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 18316 1.73 - 3.47: 1348 3.47 - 5.20: 206 5.20 - 6.94: 31 6.94 - 8.67: 9 Bond angle restraints: 19910 Sorted by residual: angle pdb=" N3 DT T 5 " pdb=" C4 DT T 5 " pdb=" O4 DT T 5 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" O4 DT T 5 " pdb=" C4 DT T 5 " pdb=" C5 DT T 5 " ideal model delta sigma weight residual 124.90 121.86 3.04 7.00e-01 2.04e+00 1.88e+01 angle pdb=" N3 DT N 13 " pdb=" C4 DT N 13 " pdb=" O4 DT N 13 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT T 2 " pdb=" C4 DT T 2 " pdb=" O4 DT T 2 " ideal model delta sigma weight residual 119.90 122.24 -2.34 6.00e-01 2.78e+00 1.53e+01 angle pdb=" N3 DT T 11 " pdb=" C4 DT T 11 " pdb=" O4 DT T 11 " ideal model delta sigma weight residual 119.90 122.24 -2.34 6.00e-01 2.78e+00 1.52e+01 ... (remaining 19905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 7942 25.98 - 51.96: 430 51.96 - 77.94: 93 77.94 - 103.93: 7 103.93 - 129.91: 2 Dihedral angle restraints: 8474 sinusoidal: 4494 harmonic: 3980 Sorted by residual: dihedral pdb=" CA ARG P1279 " pdb=" C ARG P1279 " pdb=" N VAL P1280 " pdb=" CA VAL P1280 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C4' A R 42 " pdb=" C3' A R 42 " pdb=" O3' A R 42 " pdb=" P G R 43 " ideal model delta sinusoidal sigma weight residual 220.00 90.09 129.91 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" CA ALA P1215 " pdb=" C ALA P1215 " pdb=" N SER P1216 " pdb=" CA SER P1216 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1925 0.066 - 0.131: 286 0.131 - 0.197: 56 0.197 - 0.262: 3 0.262 - 0.328: 1 Chirality restraints: 2271 Sorted by residual: chirality pdb=" C3' A R 46 " pdb=" C4' A R 46 " pdb=" O3' A R 46 " pdb=" C2' A R 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1' 2YR T 6 " pdb=" C2' 2YR T 6 " pdb=" N1 2YR T 6 " pdb=" O4' 2YR T 6 " both_signs ideal model delta sigma weight residual False 2.24 2.46 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' A R 42 " pdb=" C4' A R 42 " pdb=" O3' A R 42 " pdb=" C2' A R 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2268 not shown) Planarity restraints: 2073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 302 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C LEU P 302 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU P 302 " 0.030 2.00e-02 2.50e+03 pdb=" N SER P 303 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 32 " 0.033 2.00e-02 2.50e+03 2.30e-02 1.46e+01 pdb=" N9 A R 32 " -0.063 2.00e-02 2.50e+03 pdb=" C8 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A R 32 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A R 32 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A R 32 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A R 32 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A R 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A R 32 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 284 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ASP P 284 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP P 284 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN P 285 " 0.022 2.00e-02 2.50e+03 ... (remaining 2070 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1231 2.75 - 3.28: 13094 3.28 - 3.82: 23738 3.82 - 4.36: 29500 4.36 - 4.90: 46257 Nonbonded interactions: 113820 Sorted by model distance: nonbonded pdb=" O LEU P 101 " pdb=" O2' A R 47 " model vdw 2.207 3.040 nonbonded pdb=" NH2 ARG P 820 " pdb=" OD1 ASP P 825 " model vdw 2.252 3.120 nonbonded pdb=" NZ LYS P 742 " pdb=" OP1 C R 67 " model vdw 2.269 3.120 nonbonded pdb=" O LYS P 652 " pdb=" NH1 ARG P 655 " model vdw 2.279 3.120 nonbonded pdb=" ND2 ASN P 556 " pdb=" O LYS P 558 " model vdw 2.283 3.120 ... (remaining 113815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.380 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.007 0.124 14347 Z= 0.388 Angle : 0.995 8.673 19910 Z= 0.598 Chirality : 0.050 0.328 2271 Planarity : 0.006 0.046 2073 Dihedral : 15.253 129.907 5900 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.20), residues: 1349 helix: -0.90 (0.17), residues: 655 sheet: -0.85 (0.46), residues: 125 loop : -0.94 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 66 TYR 0.021 0.002 TYR P 812 PHE 0.026 0.003 PHE P 405 TRP 0.017 0.002 TRP P 476 HIS 0.010 0.002 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.39 (14345) covalent geometry : angle 0.99499 / 0.60 (19910) hydrogen bonds : bond 0.13469 / 14.76 ( 611) hydrogen bonds : angle 5.75591 / 6.76 ( 1672) Misc. bond : bond 0.03671 / 1.84 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8311 (mt) cc_final: 0.8101 (mp) REVERT: P 338 LEU cc_start: 0.9035 (mt) cc_final: 0.8757 (mp) REVERT: P 816 LEU cc_start: 0.8846 (mt) cc_final: 0.8288 (mt) REVERT: P 822 MET cc_start: 0.8273 (mmp) cc_final: 0.7903 (tpp) REVERT: P 841 ILE cc_start: 0.8985 (mm) cc_final: 0.8745 (mp) REVERT: P 930 HIS cc_start: 0.7620 (m90) cc_final: 0.7208 (m90) REVERT: P 1037 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7624 (p90) REVERT: P 1180 ASP cc_start: 0.7305 (m-30) cc_final: 0.7077 (m-30) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.1577 time to fit residues: 53.7074 Evaluate side-chains 97 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1037 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 690 ASN ** P 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 698 HIS P1066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.106116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077313 restraints weight = 29709.188| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.30 r_work: 0.3050 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14347 Z= 0.145 Angle : 0.606 8.699 19910 Z= 0.329 Chirality : 0.041 0.216 2271 Planarity : 0.004 0.050 2073 Dihedral : 16.060 128.545 3025 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.07 % Allowed : 8.56 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1349 helix: 0.59 (0.20), residues: 660 sheet: -0.78 (0.44), residues: 127 loop : -0.64 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P1122 TYR 0.013 0.001 TYR P 155 PHE 0.011 0.001 PHE P 446 TRP 0.009 0.001 TRP P 476 HIS 0.005 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14345) covalent geometry : angle 0.60643 / 0.33 (19910) hydrogen bonds : bond 0.04841 / 4.99 ( 611) hydrogen bonds : angle 4.82003 / 5.57 ( 1672) Misc. bond : bond 0.00769 / 0.38 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8462 (mt) cc_final: 0.8216 (mp) REVERT: P 534 MET cc_start: 0.7919 (mmm) cc_final: 0.6608 (ptt) REVERT: P 707 ASP cc_start: 0.7413 (m-30) cc_final: 0.7195 (m-30) REVERT: P 781 MET cc_start: 0.8186 (mmm) cc_final: 0.7485 (mmm) REVERT: P 816 LEU cc_start: 0.9038 (mt) cc_final: 0.8492 (mt) REVERT: P 879 MET cc_start: 0.7568 (mmm) cc_final: 0.7011 (mtp) REVERT: P 930 HIS cc_start: 0.8117 (m90) cc_final: 0.7749 (m90) REVERT: P 1037 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7735 (p90) REVERT: P 1180 ASP cc_start: 0.8364 (m-30) cc_final: 0.8161 (m-30) outliers start: 13 outliers final: 5 residues processed: 112 average time/residue: 0.1259 time to fit residues: 20.4561 Evaluate side-chains 85 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 96 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 100 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 194 GLN ** P 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074881 restraints weight = 29786.430| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.28 r_work: 0.3000 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14347 Z= 0.152 Angle : 0.554 7.976 19910 Z= 0.300 Chirality : 0.040 0.312 2271 Planarity : 0.003 0.052 2073 Dihedral : 16.186 132.087 3023 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.48 % Allowed : 10.29 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1349 helix: 1.16 (0.20), residues: 658 sheet: -0.73 (0.46), residues: 117 loop : -0.42 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 832 TYR 0.014 0.002 TYR P 155 PHE 0.014 0.001 PHE P1008 TRP 0.010 0.001 TRP P 476 HIS 0.005 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (14345) covalent geometry : angle 0.55435 / 0.30 (19910) hydrogen bonds : bond 0.04182 / 4.29 ( 611) hydrogen bonds : angle 4.52913 / 5.22 ( 1672) Misc. bond : bond 0.00479 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8307 (m-30) cc_final: 0.7933 (t0) REVERT: P 216 LEU cc_start: 0.8535 (mt) cc_final: 0.8267 (mp) REVERT: P 534 MET cc_start: 0.7821 (mmm) cc_final: 0.6554 (ptt) REVERT: P 775 LYS cc_start: 0.8870 (mptt) cc_final: 0.8526 (mmtm) REVERT: P 805 GLN cc_start: 0.8971 (mt0) cc_final: 0.8743 (mt0) REVERT: P 879 MET cc_start: 0.7737 (mmm) cc_final: 0.7381 (mmm) REVERT: P 930 HIS cc_start: 0.8196 (m90) cc_final: 0.7777 (m90) REVERT: P 1037 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7804 (p90) outliers start: 18 outliers final: 9 residues processed: 99 average time/residue: 0.1401 time to fit residues: 19.8352 Evaluate side-chains 76 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1042 ILE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.0570 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075519 restraints weight = 29773.519| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.30 r_work: 0.3055 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14347 Z= 0.115 Angle : 0.503 7.255 19910 Z= 0.274 Chirality : 0.038 0.221 2271 Planarity : 0.003 0.049 2073 Dihedral : 16.198 131.676 3023 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.23 % Allowed : 10.70 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1349 helix: 1.38 (0.20), residues: 658 sheet: -0.77 (0.44), residues: 126 loop : -0.34 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 783 TYR 0.012 0.001 TYR P 155 PHE 0.013 0.001 PHE P1008 TRP 0.008 0.001 TRP P 476 HIS 0.003 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (14345) covalent geometry : angle 0.50268 / 0.27 (19910) hydrogen bonds : bond 0.03787 / 3.87 ( 611) hydrogen bonds : angle 4.37544 / 5.04 ( 1672) Misc. bond : bond 0.00035 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8180 (m-30) cc_final: 0.7898 (t0) REVERT: P 216 LEU cc_start: 0.8494 (mt) cc_final: 0.8244 (mp) REVERT: P 534 MET cc_start: 0.7707 (mmm) cc_final: 0.6461 (ptt) REVERT: P 775 LYS cc_start: 0.8833 (mptt) cc_final: 0.8481 (mppt) REVERT: P 789 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8796 (mmmt) REVERT: P 879 MET cc_start: 0.7698 (mmm) cc_final: 0.7240 (mpp) REVERT: P 930 HIS cc_start: 0.8088 (m90) cc_final: 0.7660 (m90) REVERT: P 1037 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7800 (p90) REVERT: P 1180 ASP cc_start: 0.8330 (m-30) cc_final: 0.7969 (m-30) outliers start: 15 outliers final: 8 residues processed: 90 average time/residue: 0.1243 time to fit residues: 16.7357 Evaluate side-chains 75 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 1036 TYR Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 119 optimal weight: 0.0670 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 194 GLN ** P 692 ASN ** 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 = 0.3708 r_free = 0.3708 target = 0.103216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074301 restraints weight = 29926.596| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.28 r_work: 0.3030 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14347 Z= 0.135 Angle : 0.504 9.779 19910 Z= 0.272 Chirality : 0.038 0.225 2271 Planarity : 0.003 0.047 2073 Dihedral : 16.198 132.711 3023 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.23 % Allowed : 10.62 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1349 helix: 1.47 (0.20), residues: 663 sheet: -0.73 (0.44), residues: 126 loop : -0.35 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 832 TYR 0.013 0.001 TYR P 155 PHE 0.013 0.001 PHE P1008 TRP 0.009 0.001 TRP P 476 HIS 0.004 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14345) covalent geometry : angle 0.50444 / 0.27 (19910) hydrogen bonds : bond 0.03648 / 3.77 ( 611) hydrogen bonds : angle 4.34650 / 5.03 ( 1672) Misc. bond : bond 0.00042 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8280 (m-30) cc_final: 0.7969 (t0) REVERT: P 216 LEU cc_start: 0.8476 (mt) cc_final: 0.8222 (mp) REVERT: P 534 MET cc_start: 0.7773 (mmm) cc_final: 0.6519 (ptt) REVERT: P 789 LYS cc_start: 0.9197 (ttpt) cc_final: 0.8805 (mmmt) REVERT: P 879 MET cc_start: 0.7769 (mmm) cc_final: 0.7206 (mmm) REVERT: P 930 HIS cc_start: 0.8220 (m90) cc_final: 0.7708 (m90) REVERT: P 1037 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7903 (p90) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 0.1257 time to fit residues: 15.7274 Evaluate side-chains 69 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 663 SER Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1149 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 118 optimal weight: 0.0060 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.102783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.073749 restraints weight = 29754.788| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.28 r_work: 0.3018 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14347 Z= 0.137 Angle : 0.501 6.091 19910 Z= 0.270 Chirality : 0.038 0.224 2271 Planarity : 0.003 0.046 2073 Dihedral : 16.199 132.739 3023 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 11.03 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.23), residues: 1349 helix: 1.51 (0.20), residues: 664 sheet: -0.66 (0.45), residues: 127 loop : -0.27 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 832 TYR 0.022 0.001 TYR P1016 PHE 0.014 0.001 PHE P1008 TRP 0.009 0.001 TRP P 476 HIS 0.004 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14345) covalent geometry : angle 0.50058 / 0.27 (19910) hydrogen bonds : bond 0.03557 / 3.70 ( 611) hydrogen bonds : angle 4.33354 / 4.99 ( 1672) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8287 (m-30) cc_final: 0.7960 (t0) REVERT: P 216 LEU cc_start: 0.8516 (mt) cc_final: 0.8258 (mp) REVERT: P 534 MET cc_start: 0.7722 (mmm) cc_final: 0.6525 (ptt) REVERT: P 775 LYS cc_start: 0.8744 (mptt) cc_final: 0.8493 (mmtm) REVERT: P 781 MET cc_start: 0.8400 (mmm) cc_final: 0.7954 (mtp) REVERT: P 789 LYS cc_start: 0.9242 (ttpt) cc_final: 0.8868 (mmmt) REVERT: P 879 MET cc_start: 0.8001 (mmm) cc_final: 0.7599 (mmm) REVERT: P 930 HIS cc_start: 0.8230 (m90) cc_final: 0.7699 (m90) REVERT: P 1037 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7925 (p90) REVERT: P 1180 ASP cc_start: 0.8404 (m-30) cc_final: 0.8113 (m-30) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.1146 time to fit residues: 14.4291 Evaluate side-chains 73 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 663 SER Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 708 ILE Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1149 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074674 restraints weight = 29664.775| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.24 r_work: 0.3039 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14347 Z= 0.110 Angle : 0.495 7.471 19910 Z= 0.268 Chirality : 0.037 0.223 2271 Planarity : 0.003 0.046 2073 Dihedral : 16.162 132.925 3023 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.15 % Allowed : 11.93 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1349 helix: 1.60 (0.20), residues: 663 sheet: -0.65 (0.44), residues: 127 loop : -0.24 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 832 TYR 0.010 0.001 TYR P 155 PHE 0.013 0.001 PHE P1008 TRP 0.007 0.001 TRP P 476 HIS 0.004 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14345) covalent geometry : angle 0.49549 / 0.27 (19910) hydrogen bonds : bond 0.03379 / 3.51 ( 611) hydrogen bonds : angle 4.30528 / 4.97 ( 1672) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8484 (mt) cc_final: 0.8231 (mp) REVERT: P 775 LYS cc_start: 0.8763 (mptt) cc_final: 0.8505 (mmtm) REVERT: P 789 LYS cc_start: 0.9248 (ttpt) cc_final: 0.8874 (mmmt) REVERT: P 879 MET cc_start: 0.7938 (mmm) cc_final: 0.7523 (mmm) REVERT: P 930 HIS cc_start: 0.8220 (m90) cc_final: 0.7713 (m90) REVERT: P 1037 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7927 (p90) outliers start: 14 outliers final: 10 residues processed: 80 average time/residue: 0.1123 time to fit residues: 14.0841 Evaluate side-chains 70 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 1036 TYR Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 690 ASN P 758 ASN P1261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.103481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074519 restraints weight = 29566.654| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.27 r_work: 0.3037 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14347 Z= 0.111 Angle : 0.488 7.639 19910 Z= 0.264 Chirality : 0.037 0.224 2271 Planarity : 0.003 0.045 2073 Dihedral : 16.143 133.750 3023 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 11.19 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.23), residues: 1349 helix: 1.63 (0.20), residues: 664 sheet: -0.64 (0.44), residues: 127 loop : -0.19 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 832 TYR 0.011 0.001 TYR P 815 PHE 0.013 0.001 PHE P1008 TRP 0.007 0.001 TRP P 476 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14345) covalent geometry : angle 0.48843 / 0.26 (19910) hydrogen bonds : bond 0.03313 / 3.45 ( 611) hydrogen bonds : angle 4.28151 / 4.93 ( 1672) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8500 (mt) cc_final: 0.8251 (mp) REVERT: P 534 MET cc_start: 0.7569 (mmm) cc_final: 0.6253 (ptt) REVERT: P 584 GLU cc_start: 0.6941 (pm20) cc_final: 0.6383 (tm-30) REVERT: P 775 LYS cc_start: 0.8744 (mptt) cc_final: 0.8475 (mmtm) REVERT: P 789 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8878 (mmmt) REVERT: P 879 MET cc_start: 0.7919 (mmm) cc_final: 0.7541 (mmm) REVERT: P 930 HIS cc_start: 0.8240 (m90) cc_final: 0.7765 (m90) outliers start: 21 outliers final: 15 residues processed: 83 average time/residue: 0.1138 time to fit residues: 14.7171 Evaluate side-chains 77 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 663 SER Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 708 ILE Chi-restraints excluded: chain P residue 801 VAL Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1036 TYR Chi-restraints excluded: chain P residue 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.100465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071178 restraints weight = 29723.297| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.29 r_work: 0.2974 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14347 Z= 0.201 Angle : 0.568 13.424 19910 Z= 0.300 Chirality : 0.040 0.231 2271 Planarity : 0.004 0.044 2073 Dihedral : 16.247 133.990 3021 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.56 % Allowed : 11.19 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.23), residues: 1349 helix: 1.50 (0.20), residues: 663 sheet: -0.84 (0.44), residues: 127 loop : -0.16 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 152 TYR 0.016 0.002 TYR P 155 PHE 0.015 0.002 PHE P 916 TRP 0.014 0.002 TRP P1126 HIS 0.005 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (14345) covalent geometry : angle 0.56794 / 0.30 (19910) hydrogen bonds : bond 0.03817 / 3.97 ( 611) hydrogen bonds : angle 4.44012 / 5.09 ( 1672) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8651 (mt) cc_final: 0.8387 (mp) REVERT: P 775 LYS cc_start: 0.8781 (mptt) cc_final: 0.8469 (mmtm) REVERT: P 789 LYS cc_start: 0.9268 (ttpt) cc_final: 0.8892 (mmmt) REVERT: P 806 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8581 (tp) REVERT: P 879 MET cc_start: 0.7995 (mmm) cc_final: 0.7616 (mmm) REVERT: P 930 HIS cc_start: 0.8389 (m90) cc_final: 0.7790 (m90) outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.1180 time to fit residues: 13.9835 Evaluate side-chains 76 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 95 ASP Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 663 SER Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 708 ILE Chi-restraints excluded: chain P residue 801 VAL Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1036 TYR Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1261 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 118 optimal weight: 0.0060 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074139 restraints weight = 29482.879| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.27 r_work: 0.3027 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14347 Z= 0.106 Angle : 0.510 13.928 19910 Z= 0.271 Chirality : 0.037 0.223 2271 Planarity : 0.003 0.044 2073 Dihedral : 16.165 133.341 3021 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.07 % Allowed : 11.69 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1349 helix: 1.64 (0.20), residues: 664 sheet: -0.66 (0.45), residues: 127 loop : -0.09 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 494 TYR 0.015 0.001 TYR P 814 PHE 0.013 0.001 PHE P1008 TRP 0.003 0.001 TRP P 476 HIS 0.002 0.001 HIS P 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (14345) covalent geometry : angle 0.50981 / 0.27 (19910) hydrogen bonds : bond 0.03318 / 3.44 ( 611) hydrogen bonds : angle 4.35363 / 5.01 ( 1672) Misc. bond : bond 0.00009 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8568 (mt) cc_final: 0.8303 (mp) REVERT: P 584 GLU cc_start: 0.6854 (pm20) cc_final: 0.6377 (tm-30) REVERT: P 775 LYS cc_start: 0.8759 (mptt) cc_final: 0.8493 (mmtm) REVERT: P 789 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8855 (mmmt) REVERT: P 806 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8587 (tp) REVERT: P 879 MET cc_start: 0.7905 (mmm) cc_final: 0.7546 (mmm) REVERT: P 930 HIS cc_start: 0.8255 (m90) cc_final: 0.7731 (m90) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.1134 time to fit residues: 14.6529 Evaluate side-chains 78 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 597 LEU Chi-restraints excluded: chain P residue 663 SER Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 801 VAL Chi-restraints excluded: chain P residue 806 LEU Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 1036 TYR Chi-restraints excluded: chain P residue 1072 ILE Chi-restraints excluded: chain P residue 1149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 50.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070932 restraints weight = 29823.331| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.33 r_work: 0.2967 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14347 Z= 0.205 Angle : 0.580 13.887 19910 Z= 0.305 Chirality : 0.040 0.231 2271 Planarity : 0.004 0.044 2073 Dihedral : 16.223 134.229 3021 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.15 % Allowed : 12.10 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1349 helix: 1.54 (0.20), residues: 664 sheet: -0.82 (0.44), residues: 127 loop : -0.11 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 494 TYR 0.017 0.002 TYR P 155 PHE 0.016 0.002 PHE P1008 TRP 0.014 0.002 TRP P1126 HIS 0.005 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (14345) covalent geometry : angle 0.58022 / 0.30 (19910) hydrogen bonds : bond 0.03755 / 3.92 ( 611) hydrogen bonds : angle 4.43141 / 5.04 ( 1672) Misc. bond : bond 0.00063 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3043.88 seconds wall clock time: 53 minutes 10.33 seconds (3190.33 seconds total)