Starting phenix.real_space_refine on Fri Sep 11 16:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s3h_24823/09_2026/7s3h_24823.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s3h_24823/09_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_24823/09_2026/7s3h_24823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s3h_24823/09_2026/7s3h_24823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s3h_24823/09_2026/7s3h_24823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s3h_24823/09_2026/7s3h_24823.map" model { file = "/net/cci-nas-00/data/ceres_data/7s3h_24823/09_2026/7s3h_24823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s3h_24823/09_2026/7s3h_24823.cif" } 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-2.2.1-6174/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: {'RNAv2': 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: 2.08, 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: 0.65 Conformation dependent library (CDL) restraints added in 287.4 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: 0.98 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: 1.72 Time building geometry restraints manager: 0.94 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: 12888 1.87 - 3.73: 1106 3.73 - 5.60: 170 5.60 - 7.46: 19 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=" C3' DG T 7 " pdb=" O3' DG T 7 " pdb=" P DC T 8 " ideal model delta sigma weight residual 119.70 124.77 -5.07 1.20e+00 6.94e-01 1.78e+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 ... (remaining 14180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5264 17.26 - 34.51: 496 34.51 - 51.77: 266 51.77 - 69.02: 104 69.02 - 86.28: 12 Dihedral angle restraints: 6142 sinusoidal: 3112 harmonic: 3030 Sorted by residual: 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 36.35 -36.24 72.58 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" C4' U R 90 " pdb=" C3' U R 90 " pdb=" C2' U R 90 " pdb=" C1' U R 90 " ideal model delta sinusoidal sigma weight residual 36.35 -35.62 71.96 1 3.10e+00 1.04e-01 6.90e+02 dihedral pdb=" C4' G R 89 " pdb=" C3' G R 89 " pdb=" C2' G R 89 " pdb=" C1' G R 89 " ideal model delta sinusoidal sigma weight residual 36.34 -35.20 71.55 1 3.10e+00 1.04e-01 6.83e+02 ... (remaining 6139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1262 0.064 - 0.129: 270 0.129 - 0.193: 35 0.193 - 0.257: 24 0.257 - 0.321: 14 Chirality restraints: 1605 Sorted by residual: 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 -2.49 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" P G R 81 " pdb=" OP1 G R 81 " pdb=" OP2 G R 81 " pdb=" O5' G R 81 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" P G R 92 " pdb=" OP1 G R 92 " pdb=" OP2 G R 92 " pdb=" O5' G R 92 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.26e+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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.000 Find NCS groups from input model: 0.020 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:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- 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 : 1.113 9.329 14185 Z= 0.701 Chirality : 0.064 0.321 1605 Planarity : 0.007 0.073 1542 Dihedral : 17.968 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 0.00828 / 0.49 (10292) covalent geometry : angle 1.11292 / 0.70 (14185) hydrogen bonds : bond 0.14706 / 16.55 ( 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 : 0.292 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: 0.6014 time to fit residues: 151.0041 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 : 0.296 ------------------------------------------------------------------------------- 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: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 854 ASN P 926 GLN P1044 ASN P1221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.151030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.131256 restraints weight = 20026.794| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.57 r_work: 0.3951 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10294 Z= 0.181 Angle : 0.845 27.456 14185 Z= 0.416 Chirality : 0.064 0.976 1605 Planarity : 0.004 0.052 1542 Dihedral : 19.368 116.975 2008 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.46 % Allowed : 14.91 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.22), residues: 521 sheet: -0.25 (0.48), residues: 104 loop : -0.74 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P1019 TYR 0.018 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 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (10292) covalent geometry : angle 0.84496 / 0.42 (14185) hydrogen bonds : bond 0.05411 / 6.08 ( 493) hydrogen bonds : angle 4.85737 / 5.25 ( 1347) Misc. bond : bond 0.00134 / 0.07 ( 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 185 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6689 (ttm-80) REVERT: P 183 LYS cc_start: 0.7451 (mtpt) cc_final: 0.7182 (mmpt) REVERT: P 762 GLU cc_start: 0.7361 (tt0) cc_final: 0.7134 (tt0) REVERT: P 763 MET cc_start: 0.8336 (mmt) cc_final: 0.8021 (mmt) REVERT: P 1012 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7062 (p0) outliers start: 41 outliers final: 10 residues processed: 173 average time/residue: 0.5342 time to fit residues: 98.9538 Evaluate side-chains 134 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 LYS 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: 0.8980 chunk 87 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 0.0000 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 129 HIS P 160 HIS P 194 GLN ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 726 ASN P 758 ASN P 826 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.149701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.129722 restraints weight = 19954.577| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.59 r_work: 0.3931 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10294 Z= 0.155 Angle : 0.680 13.308 14185 Z= 0.351 Chirality : 0.049 0.436 1605 Planarity : 0.004 0.051 1542 Dihedral : 19.271 142.996 2006 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.20 (0.26), residues: 1022 helix: 0.88 (0.23), residues: 516 sheet: -0.08 (0.49), residues: 104 loop : -0.70 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 71 TYR 0.020 0.002 TYR P 347 PHE 0.014 0.002 PHE P1008 TRP 0.003 0.001 TRP P 18 HIS 0.011 0.002 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (10292) covalent geometry : angle 0.68013 / 0.35 (14185) hydrogen bonds : bond 0.04777 / 5.37 ( 493) hydrogen bonds : angle 4.65024 / 5.06 ( 1347) Misc. bond : bond 0.00022 / 0.01 ( 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 167 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6781 (ttm-80) REVERT: P 183 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7304 (mmpt) REVERT: P 836 TYR cc_start: 0.7665 (m-10) cc_final: 0.7410 (m-80) REVERT: P 838 VAL cc_start: 0.8111 (t) cc_final: 0.7907 (t) REVERT: P 1071 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6110 (tp30) outliers start: 36 outliers final: 15 residues processed: 155 average time/residue: 0.4810 time to fit residues: 80.3806 Evaluate side-chains 133 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 129 HIS 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 820 ARG Chi-restraints excluded: chain P residue 857 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 129 HIS ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 265 GLN P 771 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.145909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.126044 restraints weight = 19783.134| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.53 r_work: 0.3882 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10294 Z= 0.204 Angle : 0.710 11.075 14185 Z= 0.364 Chirality : 0.048 0.390 1605 Planarity : 0.004 0.040 1542 Dihedral : 19.184 134.747 2006 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.24 % Allowed : 16.43 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.25), residues: 1022 helix: 0.85 (0.22), residues: 512 sheet: 0.10 (0.49), residues: 104 loop : -0.69 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 976 TYR 0.024 0.002 TYR P 25 PHE 0.016 0.002 PHE P 290 TRP 0.003 0.001 TRP P1074 HIS 0.022 0.002 HIS P 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (10292) covalent geometry : angle 0.71032 / 0.36 (14185) hydrogen bonds : bond 0.04999 / 5.62 ( 493) hydrogen bonds : angle 4.67102 / 5.05 ( 1347) Misc. bond : bond 0.00159 / 0.08 ( 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 168 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7012 (ttm-80) REVERT: P 129 HIS cc_start: 0.6542 (OUTLIER) cc_final: 0.6172 (p90) REVERT: P 140 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7091 (mttt) REVERT: P 183 LYS cc_start: 0.7502 (mttt) cc_final: 0.7285 (mmpt) REVERT: P 795 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.6871 (pp) REVERT: P 1071 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5963 (tp30) outliers start: 39 outliers final: 15 residues processed: 152 average time/residue: 0.4789 time to fit residues: 78.8185 Evaluate side-chains 134 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 129 HIS Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 189 VAL Chi-restraints excluded: chain P residue 195 LEU 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 857 LEU Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 1029 ILE 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 1183 GLU Chi-restraints excluded: chain P residue 1280 VAL Chi-restraints excluded: chain P residue 1314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 187 GLN ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 982 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.147104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.127459 restraints weight = 19602.550| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.58 r_work: 0.3899 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10294 Z= 0.146 Angle : 0.650 9.795 14185 Z= 0.333 Chirality : 0.045 0.278 1605 Planarity : 0.004 0.047 1542 Dihedral : 19.036 134.417 2006 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.81 % Allowed : 18.50 % Favored : 77.69 % 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 (0.25), residues: 1022 helix: 0.93 (0.23), residues: 513 sheet: 0.17 (0.52), residues: 92 loop : -0.66 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 820 TYR 0.021 0.002 TYR P 25 PHE 0.033 0.001 PHE P 432 TRP 0.004 0.001 TRP P 18 HIS 0.006 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (10292) covalent geometry : angle 0.65045 / 0.33 (14185) hydrogen bonds : bond 0.04414 / 4.98 ( 493) hydrogen bonds : angle 4.59964 / 4.97 ( 1347) Misc. bond : bond 0.00036 / 0.02 ( 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 149 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7053 (ttm-80) REVERT: P 60 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5730 (mm-30) REVERT: P 129 HIS cc_start: 0.5942 (OUTLIER) cc_final: 0.5627 (p-80) REVERT: P 140 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7351 (mttp) REVERT: P 183 LYS cc_start: 0.7550 (mttt) cc_final: 0.7324 (mmpt) REVERT: P 990 ASN cc_start: 0.7901 (m-40) cc_final: 0.7640 (m-40) REVERT: P 1071 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6068 (tp30) REVERT: P 1183 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5679 (pp20) outliers start: 35 outliers final: 14 residues processed: 138 average time/residue: 0.4797 time to fit residues: 71.5046 Evaluate side-chains 124 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 129 HIS Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 195 LEU 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 321 MET Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1029 ILE 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: 0.9990 chunk 19 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4251 r_free = 0.4251 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.126478 restraints weight = 19842.694| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.53 r_work: 0.3888 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10294 Z= 0.156 Angle : 0.655 9.600 14185 Z= 0.337 Chirality : 0.044 0.271 1605 Planarity : 0.004 0.045 1542 Dihedral : 18.954 132.948 2006 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.05 % Allowed : 19.37 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1022 helix: 0.91 (0.23), residues: 518 sheet: 0.22 (0.50), residues: 92 loop : -0.64 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 139 TYR 0.020 0.002 TYR P 25 PHE 0.023 0.002 PHE P 432 TRP 0.003 0.001 TRP P 18 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (10292) covalent geometry : angle 0.65484 / 0.34 (14185) hydrogen bonds : bond 0.04422 / 4.98 ( 493) hydrogen bonds : angle 4.57056 / 4.96 ( 1347) Misc. bond : bond 0.00064 / 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 149 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7061 (ttm-80) REVERT: P 60 GLU cc_start: 0.6007 (mm-30) cc_final: 0.5623 (mm-30) REVERT: P 1071 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6124 (tp30) REVERT: P 1183 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5788 (pp20) outliers start: 28 outliers final: 11 residues processed: 138 average time/residue: 0.4829 time to fit residues: 72.2324 Evaluate side-chains 124 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 129 HIS Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 199 ASN 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 1314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 102 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 129 HIS P 187 GLN ** P 199 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.146524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126872 restraints weight = 19833.653| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.59 r_work: 0.3890 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10294 Z= 0.142 Angle : 0.638 9.221 14185 Z= 0.329 Chirality : 0.044 0.264 1605 Planarity : 0.004 0.047 1542 Dihedral : 18.859 132.396 2006 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.16 % Allowed : 20.46 % Favored : 76.39 % 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: 0.42 (0.26), residues: 1022 helix: 1.05 (0.23), residues: 514 sheet: 0.23 (0.50), residues: 92 loop : -0.62 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 139 TYR 0.020 0.001 TYR P 347 PHE 0.010 0.001 PHE P 432 TRP 0.003 0.001 TRP P 18 HIS 0.009 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (10292) covalent geometry : angle 0.63764 / 0.33 (14185) hydrogen bonds : bond 0.04169 / 4.72 ( 493) hydrogen bonds : angle 4.57223 / 5.06 ( 1347) Misc. bond : bond 0.00040 / 0.02 ( 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 150 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7242 (ttm-80) REVERT: P 1071 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6178 (tp30) REVERT: P 1183 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5737 (pp20) outliers start: 29 outliers final: 11 residues processed: 138 average time/residue: 0.4813 time to fit residues: 71.8395 Evaluate side-chains 129 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 129 HIS Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 199 ASN 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 1314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 160 HIS P 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.145760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.126041 restraints weight = 19788.631| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.54 r_work: 0.3882 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 10294 Z= 0.160 Angle : 0.658 9.426 14185 Z= 0.338 Chirality : 0.045 0.372 1605 Planarity : 0.004 0.050 1542 Dihedral : 18.849 132.213 2006 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.16 % Allowed : 20.67 % 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: 0.25 (0.26), residues: 1022 helix: 0.95 (0.23), residues: 520 sheet: 0.16 (0.50), residues: 92 loop : -0.77 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 139 TYR 0.019 0.002 TYR P 347 PHE 0.016 0.002 PHE P 432 TRP 0.003 0.001 TRP P 18 HIS 0.005 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10292) covalent geometry : angle 0.65815 / 0.34 (14185) hydrogen bonds : bond 0.04294 / 4.86 ( 493) hydrogen bonds : angle 4.58342 / 5.02 ( 1347) Misc. bond : bond 0.00076 / 0.04 ( 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 146 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: P 129 HIS cc_start: 0.5918 (OUTLIER) cc_final: 0.5696 (p90) REVERT: P 1071 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: P 1183 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5827 (pp20) outliers start: 29 outliers final: 10 residues processed: 134 average time/residue: 0.5024 time to fit residues: 72.9714 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 : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 129 HIS Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 199 ASN 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 1314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.0020 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.125085 restraints weight = 19660.937| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.52 r_work: 0.3870 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10294 Z= 0.176 Angle : 0.691 10.280 14185 Z= 0.354 Chirality : 0.046 0.359 1605 Planarity : 0.004 0.043 1542 Dihedral : 18.874 132.452 2006 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.50 % Allowed : 21.65 % Favored : 75.84 % 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: 0.15 (0.25), residues: 1022 helix: 0.86 (0.23), residues: 515 sheet: 0.21 (0.51), residues: 90 loop : -0.82 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 139 TYR 0.019 0.002 TYR P 347 PHE 0.015 0.002 PHE P 290 TRP 0.002 0.001 TRP P 883 HIS 0.006 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (10292) covalent geometry : angle 0.69124 / 0.35 (14185) hydrogen bonds : bond 0.04453 / 5.04 ( 493) hydrogen bonds : angle 4.65678 / 5.09 ( 1347) Misc. bond : bond 0.00084 / 0.04 ( 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 141 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7292 (ttm-80) REVERT: P 1071 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6147 (tp30) REVERT: P 1180 ASP cc_start: 0.6879 (m-30) cc_final: 0.6588 (m-30) outliers start: 23 outliers final: 15 residues processed: 131 average time/residue: 0.4779 time to fit residues: 67.6059 Evaluate side-chains 128 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 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 129 HIS Chi-restraints excluded: chain P residue 195 LEU 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 321 MET Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR 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 1314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 96 optimal weight: 0.0980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 187 GLN P 990 ASN P1177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.145948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.126443 restraints weight = 19733.023| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.52 r_work: 0.3890 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10294 Z= 0.146 Angle : 0.673 12.367 14185 Z= 0.344 Chirality : 0.045 0.331 1605 Planarity : 0.004 0.044 1542 Dihedral : 18.843 132.064 2006 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.18 % Allowed : 21.87 % 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: 0.23 (0.26), residues: 1022 helix: 0.98 (0.23), residues: 516 sheet: 0.22 (0.51), residues: 90 loop : -0.85 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 783 TYR 0.019 0.002 TYR P 347 PHE 0.014 0.001 PHE P 196 TRP 0.003 0.001 TRP P 18 HIS 0.014 0.001 HIS P 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (10292) covalent geometry : angle 0.67336 / 0.34 (14185) hydrogen bonds : bond 0.04115 / 4.66 ( 493) hydrogen bonds : angle 4.61292 / 5.11 ( 1347) Misc. bond : bond 0.00041 / 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 136 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 40 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7261 (ttm-80) REVERT: P 83 GLN cc_start: 0.6801 (tp40) cc_final: 0.5494 (mt0) REVERT: P 762 GLU cc_start: 0.7186 (pt0) cc_final: 0.6911 (pt0) REVERT: P 855 LYS cc_start: 0.7998 (mttp) cc_final: 0.7718 (mmtp) REVERT: P 1071 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6140 (tp30) REVERT: P 1183 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5843 (pp20) outliers start: 20 outliers final: 11 residues processed: 128 average time/residue: 0.5054 time to fit residues: 69.9144 Evaluate side-chains 121 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 199 ASN 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 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: 3.9990 chunk 97 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.144158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124426 restraints weight = 19821.921| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.52 r_work: 0.3861 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10294 Z= 0.180 Angle : 0.716 12.346 14185 Z= 0.362 Chirality : 0.046 0.309 1605 Planarity : 0.004 0.039 1542 Dihedral : 18.893 132.413 2006 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.07 % Allowed : 22.52 % Favored : 75.41 % 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 (0.26), residues: 1022 helix: 0.85 (0.23), residues: 513 sheet: 0.19 (0.50), residues: 90 loop : -0.83 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 71 TYR 0.027 0.002 TYR P 25 PHE 0.015 0.002 PHE P1313 TRP 0.005 0.001 TRP P1074 HIS 0.006 0.001 HIS P 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (10292) covalent geometry : angle 0.71580 / 0.36 (14185) hydrogen bonds : bond 0.04431 / 5.02 ( 493) hydrogen bonds : angle 4.66513 / 5.13 ( 1347) Misc. bond : bond 0.00104 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3606.15 seconds wall clock time: 62 minutes 12.91 seconds (3732.91 seconds total)