Starting phenix.real_space_refine on Sat Oct 24 17:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s38_24819/10_2026/7s38_24819.map" } resolution = 3.3 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= 0.092 sd= 0.966 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 138 5.49 5 S 25 5.16 5 C 8392 2.51 5 N 2442 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13987 Number of models: 1 Model: "" Number of chains: 5 Chain: "N" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 540 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} 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: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1855 Classifications: {'RNAv2': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 42, 'rna3p_pyr': 33} 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: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.91, per 1000 atoms: 0.21 Number of scatterers: 13987 At special positions: 0 Unit cell: (123.9, 112.35, 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 138 15.00 O 2990 8.00 N 2442 7.00 C 8392 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: 1.03 Conformation dependent library (CDL) restraints added in 492.3 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 10 sheets defined 55.3% alpha, 8.1% beta 48 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'P' and resid 59 through 94 removed outlier: 5.019A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL P 93 " --> pdb=" O GLU P 89 " (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: 3.757A 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 175 through 179 Processing helix chain 'P' and resid 180 through 197 Processing helix chain 'P' and resid 207 through 213 Processing helix chain 'P' and resid 217 through 228 Processing helix chain 'P' and resid 236 through 247 Processing helix chain 'P' and resid 252 through 257 Processing helix chain 'P' and resid 270 through 283 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 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 388 through 395 Processing helix chain 'P' and resid 404 through 410 removed outlier: 3.771A pdb=" N GLY P 408 " --> pdb=" O PHE P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 426 removed outlier: 4.177A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 436 removed outlier: 3.644A 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: 3.680A pdb=" N ASP P 608 " --> pdb=" O LYS P 604 " (cutoff:3.500A) Processing helix chain 'P' and resid 612 through 626 Processing helix chain 'P' and resid 628 through 636 Processing helix chain 'P' and resid 637 through 640 Processing helix chain 'P' and resid 646 through 654 removed outlier: 3.506A pdb=" N ARG P 654 " --> pdb=" O GLN P 650 " (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: 3.670A pdb=" N GLY P 715 " --> pdb=" O ALA P 711 " (cutoff:3.500A) removed outlier: 3.574A 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: 3.520A pdb=" N GLU P 798 " --> pdb=" O GLN P 794 " (cutoff:3.500A) Processing helix chain 'P' and resid 804 through 807 removed outlier: 3.692A 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: 3.592A pdb=" N ASN P 863 " --> pdb=" O SER P 860 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) Processing helix chain 'P' and resid 872 through 889 removed outlier: 3.800A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.495A 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: 3.678A pdb=" N LYS P 929 " --> pdb=" O ARG P 925 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 970 removed outlier: 3.923A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 980 through 1001 removed outlier: 4.445A pdb=" N ALA P 984 " --> pdb=" O ASN P 980 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 3.737A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1017 through 1022 removed outlier: 4.160A pdb=" N MET P1021 " --> pdb=" O ASP P1017 " (cutoff:3.500A) Processing helix chain 'P' and resid 1030 through 1034 removed outlier: 4.161A pdb=" N ALA P1034 " --> pdb=" O LYS P1031 " (cutoff:3.500A) Processing helix chain 'P' and resid 1041 through 1045 removed outlier: 3.635A pdb=" N ASN P1044 " --> pdb=" O ASN P1041 " (cutoff:3.500A) removed outlier: 4.385A 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 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 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: 6.613A pdb=" N ILE P 7 " --> pdb=" O VAL P 760 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLU P 762 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 6.540A 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: 9.859A pdb=" N GLU P1357 " --> pdb=" O LYS P 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS P 33 " --> pdb=" O GLU P1357 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ARG P1359 " --> pdb=" O LYS P 33 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU P 35 " --> pdb=" O ARG P1359 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP P1361 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.258A 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: 5.649A 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: 3.935A pdb=" N ALA P 538 " --> pdb=" O TYR P 529 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR P 529 " --> pdb=" O ALA P 538 " (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 942 through 943 removed outlier: 4.529A pdb=" N LYS P 942 " --> pdb=" O ILE P 950 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 1049 through 1051 Processing sheet with id=AA8, first strand: chain 'P' and resid 1063 through 1065 Processing sheet with id=AA9, first strand: chain 'P' and resid 1156 through 1167 removed outlier: 3.620A pdb=" N TYR P1141 " --> pdb=" O ILE P1166 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE P1196 " --> pdb=" O LEU P1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 1324 through 1326 519 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2639 1.33 - 1.45: 4045 1.45 - 1.57: 7518 1.57 - 1.69: 283 1.69 - 1.81: 46 Bond restraints: 14531 Sorted by residual: bond pdb=" O5' 2YR T 6 " pdb=" P 2YR T 6 " ideal model delta sigma weight residual 1.721 1.600 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C1' DC N 24 " pdb=" N1 DC N 24 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C1' DT N 13 " pdb=" N1 DT N 13 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.04e+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 1.77e+01 bond pdb=" C1' DC N 5 " pdb=" N1 DC N 5 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.73e+01 ... (remaining 14526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 18052 1.60 - 3.21: 1703 3.21 - 4.81: 367 4.81 - 6.41: 67 6.41 - 8.02: 9 Bond angle restraints: 20198 Sorted by residual: angle pdb=" O5' DG N 18 " pdb=" C5' DG N 18 " pdb=" C4' DG N 18 " ideal model delta sigma weight residual 109.40 113.30 -3.90 8.00e-01 1.56e+00 2.38e+01 angle pdb=" O4' DA N 17 " pdb=" C4' DA N 17 " pdb=" C3' DA N 17 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.30e+01 angle pdb=" N3 DT N 13 " pdb=" C4 DT N 13 " pdb=" O4 DT N 13 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O5' DG N 23 " pdb=" C5' DG N 23 " pdb=" C4' DG N 23 " ideal model delta sigma weight residual 109.40 112.86 -3.46 8.00e-01 1.56e+00 1.88e+01 angle pdb=" O4 DT N 13 " pdb=" C4 DT N 13 " pdb=" C5 DT N 13 " ideal model delta sigma weight residual 124.90 121.97 2.93 7.00e-01 2.04e+00 1.75e+01 ... (remaining 20193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 7384 16.72 - 33.44: 647 33.44 - 50.16: 324 50.16 - 66.88: 182 66.88 - 83.60: 21 Dihedral angle restraints: 8558 sinusoidal: 4578 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 -37.50 73.85 1 3.10e+00 1.04e-01 7.21e+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 -36.33 72.67 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' G R 43 " pdb=" C3' G R 43 " pdb=" C2' G R 43 " pdb=" C1' G R 43 " ideal model delta sinusoidal sigma weight residual 36.35 -36.21 72.55 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 8555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1854 0.068 - 0.136: 297 0.136 - 0.204: 54 0.204 - 0.271: 61 0.271 - 0.339: 37 Chirality restraints: 2303 Sorted by residual: chirality pdb=" C2' G R 43 " pdb=" C3' G R 43 " pdb=" O2' G R 43 " pdb=" C1' G R 43 " both_signs ideal model delta sigma weight residual False -2.79 -2.45 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" P U R 80 " pdb=" OP1 U R 80 " pdb=" OP2 U R 80 " pdb=" O5' U R 80 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" P A R 47 " pdb=" OP1 A R 47 " pdb=" OP2 A R 47 " pdb=" O5' A R 47 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2300 not shown) Planarity restraints: 2081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A R 69 " 0.028 2.00e-02 2.50e+03 2.40e-02 1.59e+01 pdb=" N9 A R 69 " -0.060 2.00e-02 2.50e+03 pdb=" C8 A R 69 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A R 69 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A R 69 " 0.008 2.00e-02 2.50e+03 pdb=" C6 A R 69 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A R 69 " 0.001 2.00e-02 2.50e+03 pdb=" N1 A R 69 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A R 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A R 69 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A R 69 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 302 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C LEU P 302 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU P 302 " 0.025 2.00e-02 2.50e+03 pdb=" N SER P 303 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 70 " 0.023 2.00e-02 2.50e+03 2.52e-02 1.42e+01 pdb=" N1 C R 70 " -0.055 2.00e-02 2.50e+03 pdb=" C2 C R 70 " 0.043 2.00e-02 2.50e+03 pdb=" O2 C R 70 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C R 70 " -0.007 2.00e-02 2.50e+03 pdb=" C4 C R 70 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C R 70 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C R 70 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C R 70 " 0.004 2.00e-02 2.50e+03 ... (remaining 2078 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1998 2.77 - 3.30: 12652 3.30 - 3.83: 23893 3.83 - 4.37: 29197 4.37 - 4.90: 46180 Nonbonded interactions: 113920 Sorted by model distance: nonbonded pdb=" O ARG P 557 " pdb=" OG SER P 590 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP P 276 " pdb=" NZ LYS P 599 " model vdw 2.246 3.120 nonbonded pdb=" NZ LYS P 742 " pdb=" OP1 C R 67 " model vdw 2.249 3.120 nonbonded pdb=" OP1 DG N 25 " pdb=" NH1 ARG P1114 " model vdw 2.263 3.120 nonbonded pdb=" NH2 ARG P 820 " pdb=" OD1 ASP P 825 " model vdw 2.268 3.120 ... (remaining 113915 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: 1.610 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.600 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 0.121 14533 Z= 0.414 Angle : 1.056 8.015 20198 Z= 0.618 Chirality : 0.074 0.339 2303 Planarity : 0.006 0.039 2081 Dihedral : 17.284 83.598 5984 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % 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: -1.38 (0.20), residues: 1349 helix: -0.83 (0.18), residues: 649 sheet: -0.48 (0.47), residues: 106 loop : -0.93 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P1210 TYR 0.025 0.002 TYR P1242 PHE 0.024 0.002 PHE P1235 TRP 0.012 0.002 TRP P1126 HIS 0.010 0.002 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.41 (14531) covalent geometry : angle 1.05560 / 0.62 (20198) hydrogen bonds : bond 0.14406 / 15.45 ( 635) hydrogen bonds : angle 5.87921 / 6.18 ( 1719) Misc. bond : bond 0.03620 / 1.81 ( 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 258 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 303 SER cc_start: 0.8172 (t) cc_final: 0.7851 (p) REVERT: P 338 LEU cc_start: 0.8379 (mt) cc_final: 0.8103 (mt) REVERT: P 465 MET cc_start: 0.8631 (ppp) cc_final: 0.8138 (ppp) REVERT: P 569 PHE cc_start: 0.7699 (m-80) cc_final: 0.7251 (m-80) REVERT: P 816 LEU cc_start: 0.8928 (mt) cc_final: 0.8604 (mt) REVERT: P 1339 THR cc_start: 0.8692 (p) cc_final: 0.8445 (p) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.1466 time to fit residues: 51.7904 Evaluate side-chains 101 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1008 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 224 ASN P 357 ASN P1254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.103171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.068705 restraints weight = 34160.939| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.22 r_work: 0.2931 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14533 Z= 0.223 Angle : 1.013 26.680 20198 Z= 0.450 Chirality : 0.086 1.403 2303 Planarity : 0.005 0.055 2081 Dihedral : 18.364 135.878 3107 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 10.12 % 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: -0.09 (0.22), residues: 1349 helix: 0.63 (0.20), residues: 661 sheet: -0.49 (0.46), residues: 107 loop : -0.67 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG P 307 TYR 0.016 0.002 TYR P1336 PHE 0.027 0.002 PHE P 575 TRP 0.004 0.001 TRP P1074 HIS 0.006 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (14531) covalent geometry : angle 1.01330 / 0.45 (20198) hydrogen bonds : bond 0.05330 / 5.56 ( 635) hydrogen bonds : angle 5.02461 / 5.40 ( 1719) Misc. bond : bond 0.00820 / 0.41 ( 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 123 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 90 MET cc_start: 0.9176 (tpp) cc_final: 0.8839 (tpp) REVERT: P 465 MET cc_start: 0.8989 (ppp) cc_final: 0.8669 (ppp) REVERT: P 696 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7777 (mp) REVERT: P 816 LEU cc_start: 0.9119 (mt) cc_final: 0.8732 (mt) REVERT: P 836 TYR cc_start: 0.7842 (m-80) cc_final: 0.6109 (m-80) REVERT: P 1155 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7999 (mmtt) outliers start: 22 outliers final: 11 residues processed: 116 average time/residue: 0.1352 time to fit residues: 22.0825 Evaluate side-chains 81 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 161 MET Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 502 LEU Chi-restraints excluded: chain P residue 605 ASP Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 714 SER Chi-restraints excluded: chain P residue 802 GLU Chi-restraints excluded: chain P residue 834 SER Chi-restraints excluded: chain P residue 887 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [145, 30, 38, 93, 44, 92, 59, 103, 62, 61, 127] chunk 145 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 62 optimal weight: 0.0770 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 357 ASN P 803 ASN P1054 ASN P1297 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067392 restraints weight = 34139.120| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.19 r_work: 0.2900 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14533 Z= 0.189 Angle : 0.789 17.493 20198 Z= 0.363 Chirality : 0.064 0.893 2303 Planarity : 0.004 0.052 2081 Dihedral : 18.426 142.678 3105 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.56 % Allowed : 11.52 % 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: 0.18 (0.22), residues: 1349 helix: 0.91 (0.20), residues: 669 sheet: -0.41 (0.42), residues: 136 loop : -0.64 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 215 TYR 0.015 0.001 TYR P1336 PHE 0.017 0.002 PHE P 518 TRP 0.004 0.001 TRP P 883 HIS 0.004 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (14531) covalent geometry : angle 0.78881 / 0.36 (20198) hydrogen bonds : bond 0.04816 / 4.99 ( 635) hydrogen bonds : angle 4.73358 / 5.05 ( 1719) Misc. bond : bond 0.00690 / 0.35 ( 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 93 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 90 MET cc_start: 0.9157 (tpp) cc_final: 0.8808 (tpp) REVERT: P 696 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7740 (mp) REVERT: P 816 LEU cc_start: 0.9207 (mt) cc_final: 0.8819 (mt) REVERT: P 836 TYR cc_start: 0.7509 (m-80) cc_final: 0.6107 (m-80) REVERT: P 1021 MET cc_start: 0.8036 (mmt) cc_final: 0.7833 (mmm) REVERT: P 1037 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8082 (p90) REVERT: P 1155 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8067 (mmtt) REVERT: P 1213 MET cc_start: 0.8787 (mtp) cc_final: 0.8540 (mtm) outliers start: 19 outliers final: 8 residues processed: 88 average time/residue: 0.1251 time to fit residues: 16.1937 Evaluate side-chains 71 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 161 MET Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 802 GLU Chi-restraints excluded: chain P residue 887 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [125, 104, 113, 62, 36, 110, 13, 101, 91, 137, 46] chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 758 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.101373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.066731 restraints weight = 34519.339| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.16 r_work: 0.2889 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14533 Z= 0.183 Angle : 0.726 12.533 20198 Z= 0.339 Chirality : 0.055 0.637 2303 Planarity : 0.004 0.052 2081 Dihedral : 18.419 139.435 3105 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.81 % Allowed : 11.85 % Favored : 86.34 % 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: 0.38 (0.23), residues: 1349 helix: 1.05 (0.20), residues: 671 sheet: -0.22 (0.43), residues: 136 loop : -0.53 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 424 TYR 0.015 0.001 TYR P1336 PHE 0.013 0.001 PHE P1008 TRP 0.005 0.001 TRP P 883 HIS 0.003 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (14531) covalent geometry : angle 0.72585 / 0.34 (20198) hydrogen bonds : bond 0.04515 / 4.68 ( 635) hydrogen bonds : angle 4.59297 / 4.94 ( 1719) Misc. bond : bond 0.00140 / 0.07 ( 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 95 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 185 PHE cc_start: 0.8240 (t80) cc_final: 0.7847 (t80) REVERT: P 568 TYR cc_start: 0.8271 (t80) cc_final: 0.7857 (t80) REVERT: P 693 PHE cc_start: 0.8458 (t80) cc_final: 0.8173 (t80) REVERT: P 696 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7775 (mp) REVERT: P 816 LEU cc_start: 0.9276 (mt) cc_final: 0.8893 (mt) REVERT: P 836 TYR cc_start: 0.7601 (m-80) cc_final: 0.6081 (m-80) REVERT: P 1037 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8116 (p90) REVERT: P 1155 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8093 (mmtt) REVERT: P 1213 MET cc_start: 0.8912 (mtp) cc_final: 0.8654 (mtm) outliers start: 22 outliers final: 9 residues processed: 91 average time/residue: 0.1254 time to fit residues: 16.7536 Evaluate side-chains 77 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 277 ASN Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 802 GLU Chi-restraints excluded: chain P residue 834 SER Chi-restraints excluded: chain P residue 887 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [83, 74, 125, 140, 122, 4, 24, 103, 95, 62, 120] chunk 83 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 342 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 = 0.3744 r_free = 0.3744 target = 0.101739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067101 restraints weight = 34327.583| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.16 r_work: 0.2896 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14533 Z= 0.151 Angle : 0.670 12.776 20198 Z= 0.314 Chirality : 0.051 0.417 2303 Planarity : 0.003 0.051 2081 Dihedral : 18.402 138.884 3105 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.65 % Allowed : 12.26 % Favored : 86.09 % 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: 1.26 (0.20), residues: 671 sheet: -0.14 (0.44), residues: 136 loop : -0.42 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 220 TYR 0.022 0.001 TYR P 594 PHE 0.018 0.001 PHE P 569 TRP 0.005 0.001 TRP P 659 HIS 0.003 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (14531) covalent geometry : angle 0.66996 / 0.31 (20198) hydrogen bonds : bond 0.04082 / 4.21 ( 635) hydrogen bonds : angle 4.45536 / 4.79 ( 1719) Misc. bond : bond 0.00026 / 0.01 ( 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 98 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 90 MET cc_start: 0.9282 (tpp) cc_final: 0.8928 (tpp) REVERT: P 185 PHE cc_start: 0.8278 (t80) cc_final: 0.7898 (t80) REVERT: P 465 MET cc_start: 0.9096 (ppp) cc_final: 0.8760 (ppp) REVERT: P 568 TYR cc_start: 0.8166 (t80) cc_final: 0.7884 (t80) REVERT: P 693 PHE cc_start: 0.8454 (t80) cc_final: 0.8231 (t80) REVERT: P 696 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7712 (mp) REVERT: P 816 LEU cc_start: 0.9317 (mt) cc_final: 0.8948 (mt) REVERT: P 836 TYR cc_start: 0.7492 (m-80) cc_final: 0.6048 (m-80) REVERT: P 1037 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8164 (p90) REVERT: P 1155 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8073 (mmtt) REVERT: P 1213 MET cc_start: 0.8928 (mtp) cc_final: 0.8662 (mtm) outliers start: 20 outliers final: 8 residues processed: 94 average time/residue: 0.1241 time to fit residues: 17.0045 Evaluate side-chains 78 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 277 ASN Chi-restraints excluded: chain P residue 647 VAL Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [106, 79, 124, 2, 129, 22, 65, 133, 47, 114, 9] chunk 106 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 342 GLN ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.065900 restraints weight = 34037.898| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.15 r_work: 0.2870 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14533 Z= 0.173 Angle : 0.676 12.049 20198 Z= 0.318 Chirality : 0.050 0.361 2303 Planarity : 0.004 0.050 2081 Dihedral : 18.351 138.441 3105 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.32 % Allowed : 12.51 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.67 (0.23), residues: 1349 helix: 1.29 (0.20), residues: 670 sheet: -0.15 (0.45), residues: 136 loop : -0.38 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 671 TYR 0.026 0.001 TYR P 594 PHE 0.013 0.001 PHE P1008 TRP 0.006 0.001 TRP P 659 HIS 0.003 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (14531) covalent geometry : angle 0.67618 / 0.32 (20198) hydrogen bonds : bond 0.04080 / 4.26 ( 635) hydrogen bonds : angle 4.38616 / 4.78 ( 1719) Misc. bond : bond 0.00059 / 0.03 ( 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 85 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 185 PHE cc_start: 0.8292 (t80) cc_final: 0.7910 (t80) REVERT: P 465 MET cc_start: 0.9147 (ppp) cc_final: 0.8809 (ppp) REVERT: P 568 TYR cc_start: 0.8236 (t80) cc_final: 0.7672 (t80) REVERT: P 696 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7735 (mp) REVERT: P 782 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8913 (ptpt) REVERT: P 816 LEU cc_start: 0.9294 (mt) cc_final: 0.8939 (mt) REVERT: P 836 TYR cc_start: 0.7439 (m-80) cc_final: 0.6118 (m-80) REVERT: P 1037 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8140 (p90) REVERT: P 1155 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8059 (mmtt) REVERT: P 1213 MET cc_start: 0.8961 (mtp) cc_final: 0.8701 (mtm) outliers start: 16 outliers final: 6 residues processed: 83 average time/residue: 0.1218 time to fit residues: 15.0957 Evaluate side-chains 72 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 277 ASN Chi-restraints excluded: chain P residue 692 ASN Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [119, 13, 24, 11, 58, 12, 112, 107, 125, 133, 114] chunk 119 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.0170 chunk 12 optimal weight: 0.0970 chunk 112 optimal weight: 3.9990 chunk 107 optimal weight: 0.0770 chunk 125 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 342 GLN ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.101930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069827 restraints weight = 34044.328| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.21 r_work: 0.2880 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14533 Z= 0.122 Angle : 0.639 10.209 20198 Z= 0.300 Chirality : 0.048 0.313 2303 Planarity : 0.003 0.048 2081 Dihedral : 18.314 136.899 3105 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.91 % Allowed : 13.25 % Favored : 85.84 % 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: 0.86 (0.23), residues: 1349 helix: 1.48 (0.20), residues: 670 sheet: -0.04 (0.47), residues: 127 loop : -0.34 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 671 TYR 0.016 0.001 TYR P 594 PHE 0.013 0.001 PHE P 693 TRP 0.003 0.001 TRP P 659 HIS 0.002 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (14531) covalent geometry : angle 0.63890 / 0.30 (20198) hydrogen bonds : bond 0.03715 / 3.83 ( 635) hydrogen bonds : angle 4.32266 / 4.73 ( 1719) Misc. bond : bond 0.00027 / 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 80 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 397 ASP cc_start: 0.8791 (t0) cc_final: 0.8510 (t0) REVERT: P 465 MET cc_start: 0.8943 (ppp) cc_final: 0.8705 (ppp) REVERT: P 568 TYR cc_start: 0.8282 (t80) cc_final: 0.7860 (t80) REVERT: P 696 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7693 (mp) REVERT: P 816 LEU cc_start: 0.9294 (mt) cc_final: 0.8913 (mt) REVERT: P 836 TYR cc_start: 0.7370 (m-80) cc_final: 0.6119 (m-80) REVERT: P 1037 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8240 (p90) REVERT: P 1155 LYS cc_start: 0.8273 (mmtt) cc_final: 0.8007 (mmtt) REVERT: P 1213 MET cc_start: 0.8874 (mtp) cc_final: 0.8615 (mtm) outliers start: 11 outliers final: 6 residues processed: 78 average time/residue: 0.1248 time to fit residues: 14.5731 Evaluate side-chains 70 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 277 ASN Chi-restraints excluded: chain P residue 647 VAL Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [95, 27, 124, 13, 146, 75, 63, 78, 72, 47, 111] chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 75 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P1262 HIS ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067579 restraints weight = 34128.057| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.14 r_work: 0.2906 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14533 Z= 0.125 Angle : 0.633 10.252 20198 Z= 0.299 Chirality : 0.048 0.323 2303 Planarity : 0.003 0.048 2081 Dihedral : 18.260 136.956 3105 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.82 % Allowed : 13.25 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.23), residues: 1349 helix: 1.49 (0.20), residues: 670 sheet: -0.06 (0.47), residues: 126 loop : -0.31 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 671 TYR 0.014 0.001 TYR P 594 PHE 0.024 0.001 PHE P 185 TRP 0.004 0.001 TRP P 659 HIS 0.002 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (14531) covalent geometry : angle 0.63295 / 0.30 (20198) hydrogen bonds : bond 0.03701 / 3.83 ( 635) hydrogen bonds : angle 4.29111 / 4.69 ( 1719) Misc. bond : bond 0.00028 / 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 77 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 397 ASP cc_start: 0.8898 (t0) cc_final: 0.8487 (t0) REVERT: P 465 MET cc_start: 0.9007 (ppp) cc_final: 0.8764 (ppp) REVERT: P 568 TYR cc_start: 0.8246 (t80) cc_final: 0.7568 (t80) REVERT: P 696 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7699 (mp) REVERT: P 816 LEU cc_start: 0.9262 (mt) cc_final: 0.8893 (mt) REVERT: P 824 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (m) REVERT: P 836 TYR cc_start: 0.7269 (m-80) cc_final: 0.5923 (m-80) REVERT: P 1037 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8128 (p90) REVERT: P 1155 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8009 (mmtt) REVERT: P 1213 MET cc_start: 0.8895 (mtp) cc_final: 0.8618 (mtm) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.1112 time to fit residues: 12.7656 Evaluate side-chains 71 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 277 ASN Chi-restraints excluded: chain P residue 647 VAL Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [24, 45, 17, 23, 131, 18, 5, 2, 114, 120, 62] chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 62 optimal weight: 0.0470 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P1272 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 = 0.3744 r_free = 0.3744 target = 0.101783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067222 restraints weight = 34223.515| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.21 r_work: 0.2896 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14533 Z= 0.129 Angle : 0.633 10.171 20198 Z= 0.297 Chirality : 0.048 0.327 2303 Planarity : 0.003 0.073 2081 Dihedral : 18.221 137.044 3105 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.99 % Allowed : 13.25 % Favored : 85.76 % 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: 0.95 (0.23), residues: 1349 helix: 1.55 (0.20), residues: 670 sheet: -0.06 (0.47), residues: 126 loop : -0.28 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 220 TYR 0.014 0.001 TYR P 594 PHE 0.023 0.001 PHE P 185 TRP 0.004 0.001 TRP P 883 HIS 0.003 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (14531) covalent geometry : angle 0.63307 / 0.30 (20198) hydrogen bonds : bond 0.03625 / 3.75 ( 635) hydrogen bonds : angle 4.26784 / 4.68 ( 1719) Misc. bond : bond 0.00031 / 0.02 ( 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 74 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 279 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6694 (mt) REVERT: P 397 ASP cc_start: 0.8709 (t0) cc_final: 0.8256 (t0) REVERT: P 465 MET cc_start: 0.8881 (ppp) cc_final: 0.8655 (ppp) REVERT: P 568 TYR cc_start: 0.8123 (t80) cc_final: 0.7468 (t80) REVERT: P 816 LEU cc_start: 0.9263 (mt) cc_final: 0.8897 (mt) REVERT: P 836 TYR cc_start: 0.7190 (m-80) cc_final: 0.5928 (m-80) REVERT: P 1037 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8201 (p90) REVERT: P 1155 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7955 (mmtt) REVERT: P 1213 MET cc_start: 0.8833 (mtp) cc_final: 0.8567 (mtm) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.1194 time to fit residues: 13.3092 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 : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 277 ASN Chi-restraints excluded: chain P residue 279 LEU Chi-restraints excluded: chain P residue 643 PHE Chi-restraints excluded: chain P residue 647 VAL Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1015 VAL Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [64, 30, 68, 130, 51, 48, 65, 45, 33, 17, 118] chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 0.0010 chunk 68 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P1272 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 = 0.3756 r_free = 0.3756 target = 0.102486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070329 restraints weight = 34105.680| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.22 r_work: 0.2898 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14533 Z= 0.112 Angle : 0.622 9.787 20198 Z= 0.292 Chirality : 0.047 0.335 2303 Planarity : 0.003 0.046 2081 Dihedral : 18.180 136.650 3105 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.58 % Allowed : 13.58 % Favored : 85.84 % 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: 0.98 (0.23), residues: 1349 helix: 1.58 (0.20), residues: 670 sheet: -0.06 (0.46), residues: 127 loop : -0.27 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 671 TYR 0.013 0.001 TYR P 594 PHE 0.020 0.001 PHE P 185 TRP 0.005 0.001 TRP P 883 HIS 0.002 0.001 HIS P 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (14531) covalent geometry : angle 0.62227 / 0.29 (20198) hydrogen bonds : bond 0.03492 / 3.61 ( 635) hydrogen bonds : angle 4.25091 / 4.65 ( 1719) Misc. bond : bond 0.00019 / 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 73 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 397 ASP cc_start: 0.8715 (t0) cc_final: 0.8257 (t70) REVERT: P 465 MET cc_start: 0.8876 (ppp) cc_final: 0.8670 (ppp) REVERT: P 568 TYR cc_start: 0.8191 (t80) cc_final: 0.7472 (t80) REVERT: P 816 LEU cc_start: 0.9286 (mt) cc_final: 0.8918 (mt) REVERT: P 824 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8407 (m) REVERT: P 836 TYR cc_start: 0.7254 (m-80) cc_final: 0.5980 (m-80) REVERT: P 1037 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8183 (p90) REVERT: P 1155 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7965 (mmtt) REVERT: P 1213 MET cc_start: 0.8821 (mtp) cc_final: 0.8566 (mtm) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1319 time to fit residues: 13.7361 Evaluate side-chains 69 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 647 VAL Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 830 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1037 PHE Chi-restraints excluded: chain P residue 1257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: [141, 126, 87, 3, 117, 25, 115, 52, 19, 96, 71] chunk 141 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 193 ASN P 698 HIS ** P1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.098735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063760 restraints weight = 33936.904| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.11 r_work: 0.2816 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14533 Z= 0.254 Angle : 0.753 13.332 20198 Z= 0.353 Chirality : 0.052 0.487 2303 Planarity : 0.004 0.049 2081 Dihedral : 18.262 141.927 3105 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.32 % Allowed : 12.92 % Favored : 85.76 % 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: 1.31 (0.20), residues: 670 sheet: -0.16 (0.47), residues: 126 loop : -0.31 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG P 220 TYR 0.020 0.002 TYR P 155 PHE 0.032 0.002 PHE P 693 TRP 0.009 0.002 TRP P1126 HIS 0.006 0.001 HIS P 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 (14531) covalent geometry : angle 0.75267 / 0.35 (20198) hydrogen bonds : bond 0.04446 / 4.75 ( 635) hydrogen bonds : angle 4.40143 / 4.77 ( 1719) Misc. bond : bond 0.00045 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3646.37 seconds wall clock time: 63 minutes 7.60 seconds (3787.60 seconds total)