Starting phenix.real_space_refine on Sat Sep 12 05:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s36_24817/09_2026/7s36_24817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s36_24817/09_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_24817/09_2026/7s36_24817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s36_24817/09_2026/7s36_24817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s36_24817/09_2026/7s36_24817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s36_24817/09_2026/7s36_24817.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s36_24817/09_2026/7s36_24817.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s36_24817/09_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-2.2.1-6174/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: {'RNAv2': 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: 2.95, per 1000 atoms: 0.21 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: 0.99 Conformation dependent library (CDL) restraints added in 395.0 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: 1.82 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: 3.26 Time building geometry restraints manager: 1.34 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: 18080 1.73 - 3.47: 1517 3.47 - 5.20: 268 5.20 - 6.94: 36 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: 7818 25.98 - 51.96: 501 51.96 - 77.94: 150 77.94 - 103.93: 4 103.93 - 129.91: 1 Dihedral angle restraints: 8474 sinusoidal: 4494 harmonic: 3980 Sorted by residual: dihedral pdb=" C4' C R 11 " pdb=" C3' C R 11 " pdb=" C2' C R 11 " pdb=" C1' C R 11 " ideal model delta sinusoidal sigma weight residual 36.34 -38.84 75.18 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' A R 88 " pdb=" C3' A R 88 " pdb=" C2' A R 88 " pdb=" C1' A R 88 " ideal model delta sinusoidal sigma weight residual 36.34 -36.28 72.63 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' A R 28 " pdb=" C3' A R 28 " pdb=" C2' A R 28 " pdb=" C1' A R 28 " ideal model delta sinusoidal sigma weight residual 36.35 -36.24 72.58 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 8471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1825 0.070 - 0.140: 291 0.140 - 0.209: 57 0.209 - 0.279: 68 0.279 - 0.349: 30 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 -2.50 -2.15 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" P G R 95 " pdb=" OP1 G R 95 " pdb=" OP2 G R 95 " pdb=" O5' G R 95 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" P U R 94 " pdb=" OP1 U R 94 " pdb=" OP2 U R 94 " pdb=" O5' U R 94 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.86e+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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.320 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- 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= 0.389 Angle : 1.059 8.673 19910 Z= 0.607 Chirality : 0.076 0.349 2271 Planarity : 0.006 0.046 2073 Dihedral : 16.760 129.907 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 0.00715 / 0.39 (14345) covalent geometry : angle 1.05878 / 0.61 (19910) hydrogen bonds : bond 0.13469 / 14.86 ( 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 : 0.305 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: 0.1465 time to fit residues: 50.1391 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 : 0.480 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.106429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077725 restraints weight = 29636.673| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.28 r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14347 Z= 0.188 Angle : 1.008 26.361 19910 Z= 0.439 Chirality : 0.092 1.908 2271 Planarity : 0.004 0.049 2073 Dihedral : 17.750 140.738 3025 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.99 % Allowed : 8.81 % Favored : 90.21 % 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: -0.13 (0.22), residues: 1349 helix: 0.59 (0.20), residues: 660 sheet: -0.79 (0.44), residues: 128 loop : -0.61 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 820 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 0.00392 / 0.19 (14345) covalent geometry : angle 1.00750 / 0.44 (19910) hydrogen bonds : bond 0.04735 / 4.92 ( 611) hydrogen bonds : angle 4.79129 / 5.55 ( 1672) Misc. bond : bond 0.00147 / 0.07 ( 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 115 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8350 (m-30) cc_final: 0.7965 (t0) REVERT: P 216 LEU cc_start: 0.8494 (mt) cc_final: 0.8252 (mp) REVERT: P 534 MET cc_start: 0.7962 (mmm) cc_final: 0.6644 (ptt) REVERT: P 649 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7925 (mtmm) REVERT: P 707 ASP cc_start: 0.7448 (m-30) cc_final: 0.7232 (m-30) REVERT: P 781 MET cc_start: 0.8114 (mmm) cc_final: 0.7446 (mmm) REVERT: P 816 LEU cc_start: 0.9066 (mt) cc_final: 0.8505 (mt) REVERT: P 879 MET cc_start: 0.7606 (mmm) cc_final: 0.7116 (mtp) REVERT: P 930 HIS cc_start: 0.8163 (m90) cc_final: 0.7763 (m90) REVERT: P 1037 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7755 (p90) REVERT: P 1180 ASP cc_start: 0.8393 (m-30) cc_final: 0.8178 (m-30) outliers start: 12 outliers final: 5 residues processed: 114 average time/residue: 0.1210 time to fit residues: 20.3259 Evaluate side-chains 87 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 0.5980 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.102867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073814 restraints weight = 29940.928| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.28 r_work: 0.3026 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14347 Z= 0.213 Angle : 0.808 18.144 19910 Z= 0.370 Chirality : 0.067 1.071 2271 Planarity : 0.004 0.050 2073 Dihedral : 17.827 144.027 3023 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.48 % Allowed : 10.37 % 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: 0.34 (0.23), residues: 1349 helix: 1.08 (0.20), residues: 663 sheet: -0.86 (0.44), residues: 126 loop : -0.45 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 832 TYR 0.016 0.002 TYR P 155 PHE 0.015 0.002 PHE P1008 TRP 0.013 0.002 TRP P 476 HIS 0.007 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (14345) covalent geometry : angle 0.80765 / 0.37 (19910) hydrogen bonds : bond 0.04482 / 4.62 ( 611) hydrogen bonds : angle 4.59013 / 5.28 ( 1672) Misc. bond : bond 0.00224 / 0.11 ( 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 106 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8202 (m-30) cc_final: 0.7894 (t0) REVERT: P 216 LEU cc_start: 0.8590 (mt) cc_final: 0.8339 (mp) REVERT: P 534 MET cc_start: 0.7775 (mmm) cc_final: 0.6539 (ptt) REVERT: P 775 LYS cc_start: 0.8886 (mptt) cc_final: 0.8531 (mmtm) REVERT: P 789 LYS cc_start: 0.9183 (ttpt) cc_final: 0.8775 (mmmt) REVERT: P 879 MET cc_start: 0.7840 (mmm) cc_final: 0.7502 (mmm) REVERT: P 930 HIS cc_start: 0.8224 (m90) cc_final: 0.7774 (m90) REVERT: P 1037 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7847 (p90) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 0.1219 time to fit residues: 17.4375 Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 468 LYS Chi-restraints excluded: chain P residue 700 ASP Chi-restraints excluded: chain P residue 703 THR Chi-restraints excluded: chain P residue 804 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: 0.9980 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.0040 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.104537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075454 restraints weight = 29901.870| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.29 r_work: 0.3059 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14347 Z= 0.134 Angle : 0.695 12.010 19910 Z= 0.321 Chirality : 0.056 0.621 2271 Planarity : 0.003 0.049 2073 Dihedral : 17.747 135.681 3023 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.32 % Allowed : 11.19 % Favored : 87.49 % 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: 0.62 (0.23), residues: 1349 helix: 1.35 (0.20), residues: 663 sheet: -0.78 (0.45), 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 0.011 0.001 TYR P 450 PHE 0.014 0.001 PHE P1008 TRP 0.007 0.001 TRP P 476 HIS 0.003 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14345) covalent geometry : angle 0.69455 / 0.32 (19910) hydrogen bonds : bond 0.03908 / 3.99 ( 611) hydrogen bonds : angle 4.40633 / 5.11 ( 1672) Misc. bond : bond 0.00037 / 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 93 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8236 (m-30) cc_final: 0.7916 (t0) REVERT: P 216 LEU cc_start: 0.8506 (mt) cc_final: 0.8271 (mp) REVERT: P 534 MET cc_start: 0.7722 (mmm) cc_final: 0.6468 (ptt) REVERT: P 775 LYS cc_start: 0.8842 (mptt) cc_final: 0.8498 (mppt) REVERT: P 789 LYS cc_start: 0.9184 (ttpt) cc_final: 0.8789 (mmmt) REVERT: P 879 MET cc_start: 0.7648 (mmm) cc_final: 0.7149 (mmm) REVERT: P 930 HIS cc_start: 0.8136 (m90) cc_final: 0.7687 (m90) REVERT: P 1037 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7811 (p90) REVERT: P 1156 LYS cc_start: 0.8060 (tppt) cc_final: 0.7847 (tppt) outliers start: 16 outliers final: 7 residues processed: 91 average time/residue: 0.1075 time to fit residues: 14.6994 Evaluate side-chains 74 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 8.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 194 GLN ** P 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 758 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.102557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073307 restraints weight = 30040.628| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.29 r_work: 0.3016 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14347 Z= 0.172 Angle : 0.696 13.119 19910 Z= 0.323 Chirality : 0.054 0.603 2271 Planarity : 0.003 0.046 2073 Dihedral : 17.763 137.347 3023 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.32 % Allowed : 10.86 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.43 (0.20), residues: 663 sheet: -0.71 (0.44), residues: 127 loop : -0.30 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 832 TYR 0.020 0.002 TYR P1016 PHE 0.014 0.001 PHE P1008 TRP 0.011 0.002 TRP P 476 HIS 0.005 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (14345) covalent geometry : angle 0.69644 / 0.32 (19910) hydrogen bonds : bond 0.03943 / 4.04 ( 611) hydrogen bonds : angle 4.40107 / 5.08 ( 1672) Misc. bond : bond 0.00055 / 0.03 ( 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 88 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 177 ASP cc_start: 0.8284 (m-30) cc_final: 0.7954 (t0) REVERT: P 216 LEU cc_start: 0.8565 (mt) cc_final: 0.8316 (mp) REVERT: P 789 LYS cc_start: 0.9248 (ttpt) cc_final: 0.8839 (mmmt) REVERT: P 879 MET cc_start: 0.7672 (mmm) cc_final: 0.7130 (mmm) REVERT: P 930 HIS cc_start: 0.8299 (m90) cc_final: 0.7713 (m90) REVERT: P 1037 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (p90) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.1116 time to fit residues: 14.2730 Evaluate side-chains 72 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 804 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 1057 ILE Chi-restraints excluded: chain P residue 1072 ILE 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: 2.9990 chunk 81 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.101920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072449 restraints weight = 29953.139| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.30 r_work: 0.3003 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14347 Z= 0.188 Angle : 0.694 11.344 19910 Z= 0.324 Chirality : 0.055 0.668 2271 Planarity : 0.003 0.045 2073 Dihedral : 17.753 136.193 3023 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.65 % Allowed : 11.03 % Favored : 87.33 % 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: 0.73 (0.23), residues: 1349 helix: 1.44 (0.20), residues: 663 sheet: -0.81 (0.44), residues: 127 loop : -0.26 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 832 TYR 0.014 0.002 TYR P 155 PHE 0.015 0.001 PHE P1008 TRP 0.010 0.002 TRP P 476 HIS 0.006 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (14345) covalent geometry : angle 0.69389 / 0.32 (19910) hydrogen bonds : bond 0.03949 / 4.04 ( 611) hydrogen bonds : angle 4.42271 / 5.08 ( 1672) Misc. bond : bond 0.00042 / 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 86 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8624 (mt) cc_final: 0.8375 (mp) REVERT: P 433 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8224 (mp) REVERT: P 534 MET cc_start: 0.7685 (mmm) cc_final: 0.6324 (ptt) REVERT: P 775 LYS cc_start: 0.8702 (mptt) cc_final: 0.8392 (mmtm) REVERT: P 781 MET cc_start: 0.8054 (mmm) cc_final: 0.7546 (mtp) REVERT: P 789 LYS cc_start: 0.9264 (ttpt) cc_final: 0.8882 (mmmt) REVERT: P 822 MET cc_start: 0.8223 (mmt) cc_final: 0.7355 (tpp) REVERT: P 879 MET cc_start: 0.7829 (mmm) cc_final: 0.7441 (mmm) REVERT: P 930 HIS cc_start: 0.8334 (m90) cc_final: 0.7708 (m90) REVERT: P 1037 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7966 (p90) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.1119 time to fit residues: 14.0546 Evaluate side-chains 74 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 433 LEU 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 804 THR 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 1037 PHE 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: 0.9980 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.102431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073048 restraints weight = 29959.269| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.31 r_work: 0.3015 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3486 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= 0.153 Angle : 0.666 10.452 19910 Z= 0.311 Chirality : 0.053 0.661 2271 Planarity : 0.003 0.045 2073 Dihedral : 17.727 135.829 3023 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: 0.82 (0.23), residues: 1349 helix: 1.50 (0.20), residues: 663 sheet: -0.77 (0.44), residues: 127 loop : -0.20 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 778 TYR 0.012 0.001 TYR P 155 PHE 0.014 0.001 PHE P1008 TRP 0.008 0.001 TRP P 476 HIS 0.006 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (14345) covalent geometry : angle 0.66639 / 0.31 (19910) hydrogen bonds : bond 0.03755 / 3.83 ( 611) hydrogen bonds : angle 4.41624 / 5.04 ( 1672) Misc. bond : bond 0.00038 / 0.02 ( 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 86 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8606 (mt) cc_final: 0.8359 (mp) REVERT: P 775 LYS cc_start: 0.8736 (mptt) cc_final: 0.8412 (mmtm) REVERT: P 789 LYS cc_start: 0.9262 (ttpt) cc_final: 0.8878 (mmmt) REVERT: P 822 MET cc_start: 0.8145 (mmt) cc_final: 0.7325 (tpp) REVERT: P 879 MET cc_start: 0.7891 (mmm) cc_final: 0.7475 (mmm) REVERT: P 930 HIS cc_start: 0.8322 (m90) cc_final: 0.7748 (m90) REVERT: P 1037 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (p90) outliers start: 21 outliers final: 16 residues processed: 82 average time/residue: 0.0989 time to fit residues: 12.6094 Evaluate side-chains 78 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 482 VAL 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 804 THR 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 1037 PHE 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: 2.9990 chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 125 optimal weight: 0.0970 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072566 restraints weight = 29359.585| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.23 r_work: 0.3001 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14347 Z= 0.173 Angle : 0.679 10.054 19910 Z= 0.317 Chirality : 0.053 0.616 2271 Planarity : 0.003 0.044 2073 Dihedral : 17.735 136.091 3023 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.40 % Allowed : 11.69 % 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: 0.84 (0.23), residues: 1349 helix: 1.49 (0.20), residues: 664 sheet: -0.78 (0.44), residues: 127 loop : -0.16 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 74 TYR 0.013 0.001 TYR P 155 PHE 0.016 0.001 PHE P1008 TRP 0.010 0.001 TRP P 476 HIS 0.004 0.001 HIS P 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (14345) covalent geometry : angle 0.67857 / 0.32 (19910) hydrogen bonds : bond 0.03837 / 3.93 ( 611) hydrogen bonds : angle 4.43398 / 5.05 ( 1672) Misc. bond : bond 0.00042 / 0.02 ( 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 81 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8670 (mt) cc_final: 0.8398 (mp) REVERT: P 775 LYS cc_start: 0.8665 (mptt) cc_final: 0.8359 (mmtm) REVERT: P 789 LYS cc_start: 0.9246 (ttpt) cc_final: 0.8907 (mmmt) REVERT: P 822 MET cc_start: 0.8242 (mmt) cc_final: 0.7405 (tpp) REVERT: P 879 MET cc_start: 0.7927 (mmm) cc_final: 0.7584 (mmm) REVERT: P 930 HIS cc_start: 0.8330 (m90) cc_final: 0.7758 (m90) REVERT: P 1037 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8038 (p90) outliers start: 17 outliers final: 15 residues processed: 78 average time/residue: 0.1167 time to fit residues: 14.1488 Evaluate side-chains 75 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 801 VAL Chi-restraints excluded: chain P residue 804 THR 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 1037 PHE 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: 0.0060 chunk 31 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 6 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.104134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074725 restraints weight = 29361.287| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.25 r_work: 0.3039 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14347 Z= 0.115 Angle : 0.648 12.929 19910 Z= 0.303 Chirality : 0.051 0.587 2271 Planarity : 0.003 0.044 2073 Dihedral : 17.658 135.108 3023 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.40 % Allowed : 11.85 % 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: 0.97 (0.23), residues: 1349 helix: 1.59 (0.20), residues: 664 sheet: -0.58 (0.45), residues: 125 loop : -0.12 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 340 TYR 0.020 0.001 TYR P 814 PHE 0.014 0.001 PHE P1008 TRP 0.004 0.001 TRP P 476 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14345) covalent geometry : angle 0.64832 / 0.30 (19910) hydrogen bonds : bond 0.03557 / 3.60 ( 611) hydrogen bonds : angle 4.38583 / 5.05 ( 1672) Misc. bond : bond 0.00018 / 0.01 ( 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 88 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8580 (mt) cc_final: 0.8317 (mp) REVERT: P 775 LYS cc_start: 0.8635 (mptt) cc_final: 0.8330 (mmtm) REVERT: P 789 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8869 (mmmt) REVERT: P 822 MET cc_start: 0.8162 (mmt) cc_final: 0.7322 (tpp) REVERT: P 879 MET cc_start: 0.7854 (mmm) cc_final: 0.7501 (mmm) REVERT: P 930 HIS cc_start: 0.8290 (m90) cc_final: 0.7716 (m90) REVERT: P 1180 ASP cc_start: 0.8342 (m-30) cc_final: 0.8065 (m-30) REVERT: P 1331 ILE cc_start: 0.9108 (mp) cc_final: 0.8889 (mt) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.1178 time to fit residues: 15.6419 Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 249 THR Chi-restraints excluded: chain P residue 468 LYS 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 830 ILE Chi-restraints excluded: chain P residue 911 LEU Chi-restraints excluded: chain P residue 953 VAL 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 1163 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 0.0020 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074886 restraints weight = 29295.109| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.25 r_work: 0.3044 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14347 Z= 0.122 Angle : 0.648 13.533 19910 Z= 0.303 Chirality : 0.050 0.535 2271 Planarity : 0.003 0.044 2073 Dihedral : 17.606 135.406 3021 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.23 % Allowed : 12.18 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1349 helix: 1.62 (0.20), residues: 664 sheet: -0.55 (0.45), residues: 125 loop : -0.10 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 74 TYR 0.016 0.001 TYR P 814 PHE 0.014 0.001 PHE P1008 TRP 0.006 0.001 TRP P 476 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14345) covalent geometry : angle 0.64765 / 0.30 (19910) hydrogen bonds : bond 0.03519 / 3.58 ( 611) hydrogen bonds : angle 4.35556 / 4.99 ( 1672) Misc. bond : bond 0.00024 / 0.01 ( 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 89 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 216 LEU cc_start: 0.8577 (mt) cc_final: 0.8320 (mp) REVERT: P 584 GLU cc_start: 0.6893 (pm20) cc_final: 0.6439 (tm-30) REVERT: P 775 LYS cc_start: 0.8677 (mptt) cc_final: 0.8396 (mmtm) REVERT: P 789 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8892 (mmmt) REVERT: P 806 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8744 (mm) REVERT: P 822 MET cc_start: 0.8180 (mmt) cc_final: 0.7307 (tpp) REVERT: P 879 MET cc_start: 0.7831 (mmm) cc_final: 0.7476 (mmm) REVERT: P 930 HIS cc_start: 0.8330 (m90) cc_final: 0.7744 (m90) REVERT: P 1331 ILE cc_start: 0.9107 (mp) cc_final: 0.8888 (mt) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1271 time to fit residues: 16.9014 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 : 0.524 ------------------------------------------------------------------------------- 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 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 1163 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 0.0060 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 709 GLN 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 = 0.103212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073641 restraints weight = 29389.342| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.24 r_work: 0.3025 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14347 Z= 0.152 Angle : 0.667 13.977 19910 Z= 0.312 Chirality : 0.051 0.535 2271 Planarity : 0.003 0.044 2073 Dihedral : 17.606 135.763 3021 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.32 % Allowed : 12.26 % Favored : 86.42 % 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: 1.02 (0.23), residues: 1349 helix: 1.63 (0.20), residues: 665 sheet: -0.60 (0.44), residues: 125 loop : -0.07 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 74 TYR 0.015 0.001 TYR P 814 PHE 0.015 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 0.00343 / 0.15 (14345) covalent geometry : angle 0.66673 / 0.31 (19910) hydrogen bonds : bond 0.03645 / 3.72 ( 611) hydrogen bonds : angle 4.39964 / 5.02 ( 1672) Misc. bond : bond 0.00040 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.83 seconds wall clock time: 50 minutes 4.91 seconds (3004.91 seconds total)