Starting phenix.real_space_refine on Thu Jul 2 20:46:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s3h_24823/07_2026/7s3h_24823.map" } resolution = 2.5 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= 0.149 sd= 0.899 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 75 5.49 5 S 18 5.16 5 C 6067 2.51 5 N 1755 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9966 Number of models: 1 Model: "" Number of chains: 5 Chain: "N" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 479 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "P" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8378 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 26, 'TRANS': 1003} Chain breaks: 3 Chain: "R" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 645 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 25} 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: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 363 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.21 Number of scatterers: 9966 At special positions: 0 Unit cell: (91.35, 114.45, 116.55, 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 18 16.00 P 75 15.00 O 2051 8.00 N 1755 7.00 C 6067 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: 0.92 Conformation dependent library (CDL) restraints added in 294.7 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 55.3% alpha, 9.5% beta 32 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'P' and resid 58 through 64 Processing helix chain 'P' and resid 67 through 91 removed outlier: 4.760A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 134 through 145 removed outlier: 3.866A pdb=" N LEU P 138 " --> pdb=" O THR P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 removed outlier: 3.667A pdb=" N PHE P 164 " --> pdb=" O HIS P 160 " (cutoff:3.500A) 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 removed outlier: 3.566A 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 Processing helix chain 'P' and resid 270 through 283 Processing helix chain 'P' and resid 286 through 308 removed outlier: 4.595A pdb=" N VAL P 308 " --> pdb=" O ASP P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 343 Processing helix chain 'P' and resid 346 through 352 removed outlier: 3.593A 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 388 through 395 removed outlier: 3.545A pdb=" N LYS P 392 " --> pdb=" O GLU P 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 410 removed outlier: 3.627A pdb=" N ASN P 407 " --> pdb=" O THR P 404 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY P 408 " --> pdb=" O PHE P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 426 removed outlier: 4.072A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 436 removed outlier: 3.765A 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 719 through 726 Processing helix chain 'P' and resid 730 through 751 Processing helix chain 'P' and resid 772 through 792 removed outlier: 3.934A pdb=" N SER P 777 " --> pdb=" O GLY P 773 " (cutoff:3.500A) Processing helix chain 'P' and resid 794 through 799 removed outlier: 3.747A pdb=" N GLU P 798 " --> pdb=" O GLN P 794 " (cutoff:3.500A) Processing helix chain 'P' and resid 804 through 807 removed outlier: 3.697A 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: 3.660A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) Processing helix chain 'P' and resid 872 through 889 removed outlier: 3.876A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.548A 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 Processing helix chain 'P' and resid 959 through 970 removed outlier: 3.943A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 980 through 1001 removed outlier: 4.512A pdb=" N ALA P 984 " --> pdb=" O ASN P 980 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 3.831A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1041 through 1045 removed outlier: 3.608A pdb=" N ASN P1044 " --> pdb=" O ASN P1041 " (cutoff:3.500A) removed outlier: 4.326A 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 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 1281 removed outlier: 3.755A pdb=" N ARG P1279 " --> pdb=" O GLU P1275 " (cutoff:3.500A) 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: 6.422A pdb=" N ILE P 7 " --> pdb=" O VAL P 760 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLU P 762 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 6.253A 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: 10.091A pdb=" N GLU P1357 " --> pdb=" O LYS P 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS P 33 " --> pdb=" O GLU P1357 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ARG P1359 " --> pdb=" O LYS P 33 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU P 35 " --> pdb=" O ARG P1359 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP P1361 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 837 through 840 Processing sheet with id=AA4, first strand: chain 'P' and resid 942 through 943 removed outlier: 4.424A pdb=" N LYS P 942 " --> pdb=" O ILE P 950 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'P' and resid 1063 through 1065 Processing sheet with id=AA7, first strand: chain 'P' and resid 1156 through 1167 removed outlier: 3.618A pdb=" N TYR P1141 " --> pdb=" O ILE P1166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 1324 through 1326 415 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2536 1.34 - 1.46: 2210 1.46 - 1.58: 5360 1.58 - 1.70: 153 1.70 - 1.82: 33 Bond restraints: 10292 Sorted by residual: bond pdb=" O5' 2YR T 6 " pdb=" P 2YR T 6 " ideal model delta sigma weight residual 1.721 1.614 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C1' DT T 12 " pdb=" N1 DT T 12 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.08e+01 bond pdb=" C1' DT N 27 " pdb=" N1 DT N 27 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" C1' DC T 17 " pdb=" N1 DC T 17 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.81e+01 bond pdb=" C3' DG T 13 " pdb=" C2' DG T 13 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.79e+01 ... (remaining 10287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 12961 1.87 - 3.73: 1051 3.73 - 5.60: 153 5.60 - 7.46: 18 7.46 - 9.33: 2 Bond angle restraints: 14185 Sorted by residual: angle pdb=" N3 DT N 27 " pdb=" C4 DT N 27 " pdb=" O4 DT N 27 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT T 14 " pdb=" C4 DT T 14 " pdb=" O4 DT T 14 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O4 DT N 27 " pdb=" C4 DT N 27 " pdb=" C5 DT N 27 " ideal model delta sigma weight residual 124.90 121.91 2.99 7.00e-01 2.04e+00 1.83e+01 angle pdb=" O4 DT T 14 " pdb=" C4 DT T 14 " pdb=" C5 DT T 14 " ideal model delta sigma weight residual 124.90 121.97 2.93 7.00e-01 2.04e+00 1.75e+01 angle pdb=" O4 DT T 11 " pdb=" C4 DT T 11 " pdb=" C5 DT T 11 " ideal model delta sigma weight residual 124.90 122.15 2.75 7.00e-01 2.04e+00 1.54e+01 ... (remaining 14180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5313 17.26 - 34.51: 488 34.51 - 51.77: 246 51.77 - 69.02: 86 69.02 - 86.28: 9 Dihedral angle restraints: 6142 sinusoidal: 3112 harmonic: 3030 Sorted by residual: dihedral pdb=" CA GLU P 198 " pdb=" C GLU P 198 " pdb=" N ASN P 199 " pdb=" CA ASN P 199 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA P1215 " pdb=" C ALA P1215 " pdb=" N SER P1216 " pdb=" CA SER P1216 " ideal model delta harmonic sigma weight residual 180.00 -161.73 -18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP P 912 " pdb=" CB ASP P 912 " pdb=" CG ASP P 912 " pdb=" OD1 ASP P 912 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1127 0.050 - 0.100: 382 0.100 - 0.150: 81 0.150 - 0.200: 12 0.200 - 0.250: 3 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CB VAL P 143 " pdb=" CA VAL P 143 " pdb=" CG1 VAL P 143 " pdb=" CG2 VAL P 143 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE P 956 " pdb=" CA ILE P 956 " pdb=" CG1 ILE P 956 " pdb=" CG2 ILE P 956 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1' 2YR T 6 " pdb=" C2' 2YR T 6 " pdb=" N1 2YR T 6 " pdb=" O4' 2YR T 6 " both_signs ideal model delta sigma weight residual False 2.24 2.45 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1602 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2YR T 6 " -0.040 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" C2 2YR T 6 " -0.006 2.00e-02 2.50e+03 pdb=" C4 2YR T 6 " 0.061 2.00e-02 2.50e+03 pdb=" C5 2YR T 6 " 0.068 2.00e-02 2.50e+03 pdb=" C6 2YR T 6 " 0.028 2.00e-02 2.50e+03 pdb=" C9 2YR T 6 " -0.171 2.00e-02 2.50e+03 pdb=" N1 2YR T 6 " -0.024 2.00e-02 2.50e+03 pdb=" N3 2YR T 6 " 0.028 2.00e-02 2.50e+03 pdb=" N4 2YR T 6 " 0.101 2.00e-02 2.50e+03 pdb=" O2 2YR T 6 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 17 " 0.055 2.00e-02 2.50e+03 3.29e-02 2.99e+01 pdb=" N9 DA N 17 " -0.084 2.00e-02 2.50e+03 pdb=" C8 DA N 17 " 0.032 2.00e-02 2.50e+03 pdb=" N7 DA N 17 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA N 17 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DA N 17 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA N 17 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DA N 17 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DA N 17 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA N 17 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA N 17 " -0.021 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 3.83e-02 1.47e+01 pdb=" C ASP P 284 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP P 284 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN P 285 " -0.023 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1352 2.77 - 3.30: 9393 3.30 - 3.83: 16905 3.83 - 4.37: 20518 4.37 - 4.90: 32721 Nonbonded interactions: 80889 Sorted by model distance: nonbonded pdb=" NH2 ARG P 139 " pdb=" OE1 GLU P 418 " model vdw 2.234 3.120 nonbonded pdb=" O PHE P 846 " pdb=" OG SER P1040 " model vdw 2.247 3.040 nonbonded pdb=" NH1 ARG P 78 " pdb=" O ILE P 162 " model vdw 2.267 3.120 nonbonded pdb=" O VAL P 143 " pdb=" NE ARG P 425 " model vdw 2.270 3.120 nonbonded pdb=" OE1 GLU P1205 " pdb=" NH2 ARG P1359 " model vdw 2.275 3.120 ... (remaining 80884 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.630 Find NCS groups from input model: 0.040 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.008 0.107 10294 Z= 0.492 Angle : 1.084 9.329 14185 Z= 0.693 Chirality : 0.051 0.250 1605 Planarity : 0.007 0.073 1542 Dihedral : 17.212 86.276 4182 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % 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 (0.23), residues: 1022 helix: -0.90 (0.20), residues: 514 sheet: -0.47 (0.48), residues: 104 loop : -1.03 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 139 TYR 0.016 0.002 TYR P 362 PHE 0.031 0.003 PHE P 405 TRP 0.019 0.002 TRP P 883 HIS 0.017 0.002 HIS P1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.49 (10292) covalent geometry : angle 1.08419 / 0.69 (14185) hydrogen bonds : bond 0.14706 / 16.51 ( 493) hydrogen bonds : angle 5.70157 / 6.54 ( 1347) Misc. bond : bond 0.03302 / 1.65 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.352 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 10 ASP cc_start: 0.7147 (t70) cc_final: 0.6879 (t0) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.6442 time to fit residues: 161.9024 Evaluate side-chains 137 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 190 GLN P 194 GLN ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN P 726 ASN P 826 GLN P 854 ASN P 926 GLN P1044 ASN P1221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.150679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130680 restraints weight = 19947.639| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.60 r_work: 0.3942 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10294 Z= 0.166 Angle : 0.666 8.326 14185 Z= 0.366 Chirality : 0.045 0.304 1605 Planarity : 0.004 0.053 1542 Dihedral : 18.500 77.467 2008 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.35 % Allowed : 15.23 % Favored : 80.41 % 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 (0.25), residues: 1022 helix: 0.51 (0.22), residues: 521 sheet: -0.23 (0.48), residues: 104 loop : -0.72 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 905 TYR 0.019 0.002 TYR P 347 PHE 0.018 0.002 PHE P1008 TRP 0.005 0.001 TRP P 883 HIS 0.007 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (10292) covalent geometry : angle 0.66594 / 0.37 (14185) hydrogen bonds : bond 0.05343 / 5.97 ( 493) hydrogen bonds : angle 4.84270 / 5.24 ( 1347) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6709 (ttm-80) REVERT: P 183 LYS cc_start: 0.7503 (mtpt) cc_final: 0.7197 (mmpt) REVERT: P 763 MET cc_start: 0.8360 (mmt) cc_final: 0.8076 (mmt) REVERT: P 1012 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7050 (p0) outliers start: 40 outliers final: 9 residues processed: 171 average time/residue: 0.6022 time to fit residues: 110.4161 Evaluate side-chains 135 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1012 ASP Chi-restraints excluded: chain P residue 1042 ILE Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1277 SER Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 160 HIS ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 726 ASN P 758 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.148124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.128001 restraints weight = 19697.945| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.58 r_work: 0.3905 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10294 Z= 0.161 Angle : 0.598 8.077 14185 Z= 0.331 Chirality : 0.042 0.327 1605 Planarity : 0.004 0.041 1542 Dihedral : 18.320 82.323 2006 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.92 % Allowed : 16.32 % Favored : 79.76 % 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: 0.15 (0.26), residues: 1022 helix: 0.80 (0.22), residues: 518 sheet: -0.03 (0.49), residues: 104 loop : -0.71 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 139 TYR 0.019 0.002 TYR P 347 PHE 0.014 0.002 PHE P1008 TRP 0.003 0.001 TRP P 18 HIS 0.009 0.002 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (10292) covalent geometry : angle 0.59788 / 0.33 (14185) hydrogen bonds : bond 0.04833 / 5.42 ( 493) hydrogen bonds : angle 4.67341 / 5.09 ( 1347) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.6813 (ttm-80) REVERT: P 183 LYS cc_start: 0.7625 (mtpt) cc_final: 0.7298 (mmpt) REVERT: P 836 TYR cc_start: 0.7729 (m-10) cc_final: 0.7454 (m-80) REVERT: P 855 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7918 (mttm) REVERT: P 1071 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6169 (tp30) outliers start: 36 outliers final: 11 residues processed: 159 average time/residue: 0.5372 time to fit residues: 92.1829 Evaluate side-chains 134 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 855 LYS Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 160 HIS P 199 ASN P 265 GLN P 771 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.143312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122983 restraints weight = 19612.134| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.52 r_work: 0.3835 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10294 Z= 0.226 Angle : 0.673 7.150 14185 Z= 0.367 Chirality : 0.043 0.183 1605 Planarity : 0.005 0.048 1542 Dihedral : 18.266 88.809 2006 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.68 % Allowed : 16.65 % Favored : 78.67 % 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: 0.05 (0.25), residues: 1022 helix: 0.66 (0.22), residues: 512 sheet: 0.19 (0.51), residues: 92 loop : -0.68 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P1298 TYR 0.032 0.003 TYR P 25 PHE 0.020 0.002 PHE P1080 TRP 0.004 0.002 TRP P1074 HIS 0.008 0.002 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (10292) covalent geometry : angle 0.67298 / 0.37 (14185) hydrogen bonds : bond 0.05343 / 5.98 ( 493) hydrogen bonds : angle 4.71764 / 5.08 ( 1347) Misc. bond : bond 0.00134 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7118 (ttm-80) REVERT: P 140 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7183 (mttp) REVERT: P 183 LYS cc_start: 0.7612 (mtpt) cc_final: 0.7357 (mmpt) REVERT: P 197 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: P 795 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6868 (pp) REVERT: P 1013 TYR cc_start: 0.6858 (m-80) cc_final: 0.6613 (m-80) REVERT: P 1071 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5881 (tp30) REVERT: P 1284 ASP cc_start: 0.8241 (m-30) cc_final: 0.7951 (m-30) REVERT: P 1358 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8010 (m) outliers start: 43 outliers final: 14 residues processed: 159 average time/residue: 0.4929 time to fit residues: 84.6650 Evaluate side-chains 131 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 795 ILE Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1018 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1358 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 982 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.143618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.123395 restraints weight = 19556.575| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.51 r_work: 0.3843 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10294 Z= 0.180 Angle : 0.616 9.159 14185 Z= 0.337 Chirality : 0.041 0.219 1605 Planarity : 0.004 0.045 1542 Dihedral : 18.163 88.977 2006 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.92 % Allowed : 18.17 % Favored : 77.91 % 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: 0.08 (0.25), residues: 1022 helix: 0.73 (0.23), residues: 514 sheet: 0.10 (0.51), residues: 92 loop : -0.72 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 139 TYR 0.023 0.002 TYR P 25 PHE 0.032 0.002 PHE P 432 TRP 0.004 0.001 TRP P 18 HIS 0.006 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (10292) covalent geometry : angle 0.61557 / 0.34 (14185) hydrogen bonds : bond 0.04806 / 5.39 ( 493) hydrogen bonds : angle 4.66621 / 5.05 ( 1347) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: P 140 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7348 (mttp) REVERT: P 197 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6601 (pm20) REVERT: P 1071 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5888 (tp30) REVERT: P 1087 LEU cc_start: 0.8433 (mm) cc_final: 0.8228 (mp) REVERT: P 1183 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5367 (tt0) outliers start: 36 outliers final: 12 residues processed: 135 average time/residue: 0.5264 time to fit residues: 76.7085 Evaluate side-chains 124 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 440 ILE Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 199 ASN ** 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 = 0.4223 r_free = 0.4223 target = 0.143957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.123737 restraints weight = 19712.673| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.58 r_work: 0.3848 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10294 Z= 0.158 Angle : 0.587 7.167 14185 Z= 0.323 Chirality : 0.040 0.152 1605 Planarity : 0.004 0.086 1542 Dihedral : 18.067 88.331 2006 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.94 % Allowed : 20.46 % Favored : 76.61 % 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: 0.16 (0.25), residues: 1022 helix: 0.83 (0.23), residues: 513 sheet: 0.05 (0.50), residues: 92 loop : -0.71 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 783 TYR 0.019 0.002 TYR P 25 PHE 0.012 0.002 PHE P 196 TRP 0.005 0.001 TRP P 18 HIS 0.008 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (10292) covalent geometry : angle 0.58675 / 0.32 (14185) hydrogen bonds : bond 0.04489 / 5.06 ( 493) hydrogen bonds : angle 4.60421 / 5.03 ( 1347) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7262 (ttm-80) REVERT: P 1071 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6085 (tp30) REVERT: P 1087 LEU cc_start: 0.8464 (mm) cc_final: 0.8226 (mp) REVERT: P 1183 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5968 (pp20) outliers start: 27 outliers final: 11 residues processed: 135 average time/residue: 0.4468 time to fit residues: 65.1713 Evaluate side-chains 125 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.144080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.123902 restraints weight = 19574.127| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.57 r_work: 0.3849 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10294 Z= 0.153 Angle : 0.579 6.872 14185 Z= 0.319 Chirality : 0.039 0.166 1605 Planarity : 0.004 0.062 1542 Dihedral : 18.005 88.037 2006 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.26 % Allowed : 20.13 % Favored : 76.61 % 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: 0.25 (0.26), residues: 1022 helix: 0.97 (0.23), residues: 507 sheet: 0.12 (0.50), residues: 92 loop : -0.75 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 139 TYR 0.018 0.002 TYR P 25 PHE 0.025 0.002 PHE P 432 TRP 0.005 0.001 TRP P 18 HIS 0.006 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10292) covalent geometry : angle 0.57868 / 0.32 (14185) hydrogen bonds : bond 0.04369 / 4.92 ( 493) hydrogen bonds : angle 4.59454 / 5.04 ( 1347) Misc. bond : bond 0.00062 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7282 (ttm-80) REVERT: P 1071 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6134 (tp30) REVERT: P 1087 LEU cc_start: 0.8469 (mm) cc_final: 0.8219 (mp) REVERT: P 1183 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5912 (pp20) outliers start: 30 outliers final: 11 residues processed: 134 average time/residue: 0.4672 time to fit residues: 67.6057 Evaluate side-chains 120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.143946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.123832 restraints weight = 19603.470| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.57 r_work: 0.3847 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10294 Z= 0.150 Angle : 0.589 8.727 14185 Z= 0.323 Chirality : 0.040 0.188 1605 Planarity : 0.004 0.051 1542 Dihedral : 17.986 87.816 2006 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.72 % Allowed : 21.11 % Favored : 76.17 % 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: 0.28 (0.26), residues: 1022 helix: 1.00 (0.23), residues: 507 sheet: 0.10 (0.51), residues: 92 loop : -0.73 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 783 TYR 0.016 0.001 TYR P 347 PHE 0.012 0.001 PHE P 252 TRP 0.004 0.001 TRP P 18 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (10292) covalent geometry : angle 0.58897 / 0.32 (14185) hydrogen bonds : bond 0.04267 / 4.82 ( 493) hydrogen bonds : angle 4.57176 / 5.02 ( 1347) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7298 (ttm-80) REVERT: P 857 LEU cc_start: 0.8161 (tp) cc_final: 0.7907 (tm) REVERT: P 1071 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6195 (tp30) REVERT: P 1183 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5896 (pp20) outliers start: 25 outliers final: 12 residues processed: 126 average time/residue: 0.4925 time to fit residues: 67.3832 Evaluate side-chains 122 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.144040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.124036 restraints weight = 19541.803| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.51 r_work: 0.3854 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10294 Z= 0.146 Angle : 0.585 8.629 14185 Z= 0.320 Chirality : 0.041 0.386 1605 Planarity : 0.004 0.068 1542 Dihedral : 17.982 87.621 2006 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.83 % Allowed : 21.22 % Favored : 75.95 % 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: 0.29 (0.26), residues: 1022 helix: 1.00 (0.23), residues: 507 sheet: 0.11 (0.51), residues: 92 loop : -0.72 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 139 TYR 0.016 0.001 TYR P 271 PHE 0.013 0.001 PHE P 252 TRP 0.005 0.001 TRP P 18 HIS 0.006 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (10292) covalent geometry : angle 0.58515 / 0.32 (14185) hydrogen bonds : bond 0.04267 / 4.81 ( 493) hydrogen bonds : angle 4.56417 / 5.01 ( 1347) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7239 (ttm-80) REVERT: P 83 GLN cc_start: 0.7133 (tp40) cc_final: 0.6848 (tp40) REVERT: P 161 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.7009 (mpm) REVERT: P 1071 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6161 (tp30) REVERT: P 1087 LEU cc_start: 0.8461 (mm) cc_final: 0.8222 (mp) outliers start: 26 outliers final: 14 residues processed: 126 average time/residue: 0.4159 time to fit residues: 57.1320 Evaluate side-chains 120 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 161 MET Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 933 GLN Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 0.0770 chunk 96 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.145239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.125296 restraints weight = 19642.152| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.53 r_work: 0.3874 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10294 Z= 0.133 Angle : 0.595 10.548 14185 Z= 0.323 Chirality : 0.040 0.234 1605 Planarity : 0.004 0.069 1542 Dihedral : 17.926 86.396 2006 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.18 % Allowed : 22.85 % Favored : 74.97 % 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: 0.27 (0.26), residues: 1022 helix: 1.02 (0.23), residues: 517 sheet: 0.11 (0.50), residues: 92 loop : -0.81 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG P 139 TYR 0.016 0.001 TYR P 347 PHE 0.009 0.001 PHE P 252 TRP 0.005 0.001 TRP P 18 HIS 0.004 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10292) covalent geometry : angle 0.59484 / 0.32 (14185) hydrogen bonds : bond 0.04074 / 4.61 ( 493) hydrogen bonds : angle 4.55753 / 5.00 ( 1347) Misc. bond : bond 0.00035 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7228 (ttm-80) REVERT: P 83 GLN cc_start: 0.7088 (tp40) cc_final: 0.6824 (tp40) REVERT: P 161 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6848 (mpm) REVERT: P 1071 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6160 (tp30) REVERT: P 1219 GLU cc_start: 0.7280 (tt0) cc_final: 0.7075 (tt0) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.4959 time to fit residues: 65.5922 Evaluate side-chains 117 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 161 MET Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 321 MET Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 933 GLN Chi-restraints excluded: chain P residue 1071 GLU Chi-restraints excluded: chain P residue 1143 VAL Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1146 VAL Chi-restraints excluded: chain P residue 1157 LEU Chi-restraints excluded: chain P residue 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.142921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122869 restraints weight = 19710.453| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.52 r_work: 0.3837 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10294 Z= 0.177 Angle : 0.630 8.657 14185 Z= 0.342 Chirality : 0.041 0.239 1605 Planarity : 0.004 0.056 1542 Dihedral : 17.985 88.381 2006 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.18 % Allowed : 22.74 % Favored : 75.08 % 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: 0.18 (0.26), residues: 1022 helix: 0.91 (0.23), residues: 511 sheet: 0.13 (0.50), residues: 92 loop : -0.81 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 139 TYR 0.017 0.002 TYR P 271 PHE 0.017 0.002 PHE P 432 TRP 0.004 0.001 TRP P1074 HIS 0.007 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (10292) covalent geometry : angle 0.63004 / 0.34 (14185) hydrogen bonds : bond 0.04463 / 5.04 ( 493) hydrogen bonds : angle 4.66366 / 5.11 ( 1347) Misc. bond : bond 0.00096 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.26 seconds wall clock time: 62 minutes 55.02 seconds (3775.02 seconds total)