Starting phenix.real_space_refine on Fri Dec 8 23:12:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/12_2023/7s37_24818.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/12_2023/7s37_24818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/12_2023/7s37_24818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/12_2023/7s37_24818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/12_2023/7s37_24818.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/12_2023/7s37_24818.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.242 sd= 1.445 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 46 5.49 5 S 16 5.16 5 C 5782 2.51 5 N 1655 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9392 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 8401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8401 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 26, 'TRANS': 1006} Chain breaks: 3 Chain: "R" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 991 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 25, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 40} Chain breaks: 1 Time building chain proxies: 5.56, per 1000 atoms: 0.59 Number of scatterers: 9392 At special positions: 0 Unit cell: (86.97, 114.845, 123.765, 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 16 16.00 P 46 15.00 O 1893 8.00 N 1655 7.00 C 5782 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 56.4% alpha, 9.2% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'P' and resid 58 through 64 Processing helix chain 'P' and resid 67 through 92 removed outlier: 4.450A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 132 Processing helix chain 'P' and resid 134 through 145 removed outlier: 3.748A pdb=" N LEU P 138 " --> pdb=" O THR P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 Processing helix chain 'P' and resid 175 through 179 Processing helix chain 'P' and resid 180 through 196 Processing helix chain 'P' and resid 207 through 213 Processing helix chain 'P' and resid 217 through 228 removed outlier: 3.710A 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 306 Processing helix chain 'P' and resid 315 through 343 Processing helix chain 'P' and resid 346 through 352 removed outlier: 3.520A 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: 3.639A pdb=" N LYS P 392 " --> pdb=" O GLU P 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 410 removed outlier: 3.730A pdb=" N ASN P 407 " --> pdb=" O THR P 404 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY P 408 " --> pdb=" O PHE P 405 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE P 410 " --> pdb=" O ASN P 407 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 426 removed outlier: 4.089A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 436 removed outlier: 3.760A 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 774 through 792 Processing helix chain 'P' and resid 794 through 799 Processing helix chain 'P' and resid 804 through 807 removed outlier: 3.595A 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: 3.658A pdb=" N ASN P 863 " --> pdb=" O SER P 860 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) Processing helix chain 'P' and resid 872 through 889 removed outlier: 3.504A pdb=" N VAL P 876 " --> pdb=" O SER P 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR P 882 " --> pdb=" O LYS P 878 " (cutoff:3.500A) Processing helix chain 'P' and resid 893 through 901 Processing helix chain 'P' and resid 902 through 906 Processing helix chain 'P' and resid 909 through 922 Processing helix chain 'P' and resid 925 through 940 removed outlier: 3.550A pdb=" N LYS P 929 " --> pdb=" O ARG P 925 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 971 removed outlier: 3.994A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 980 through 1001 removed outlier: 4.527A pdb=" N ALA P 984 " --> pdb=" O ASN P 980 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 3.759A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1041 through 1045 removed outlier: 3.641A pdb=" N ASN P1044 " --> pdb=" O ASN P1041 " (cutoff:3.500A) removed outlier: 4.362A 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 1168 through 1177 removed outlier: 4.546A pdb=" N SER P1172 " --> pdb=" O ILE P1168 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER P1173 " --> pdb=" O MET P1169 " (cutoff:3.500A) Processing helix chain 'P' and resid 1177 through 1186 Processing helix chain 'P' and resid 1191 through 1195 removed outlier: 3.724A pdb=" N ILE P1195 " --> pdb=" O LYS P1192 " (cutoff:3.500A) 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 removed outlier: 3.505A pdb=" N HIS P1262 " --> pdb=" O PHE P1258 " (cutoff:3.500A) Processing helix chain 'P' and resid 1263 through 1281 removed outlier: 4.315A pdb=" N ASP P1267 " --> pdb=" O LYS P1263 " (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 1314 through 1316 No H-bonds generated for 'chain 'P' and resid 1314 through 1316' Processing helix chain 'P' and resid 1340 through 1344 Processing helix chain 'P' and resid 1363 through 1365 No H-bonds generated for 'chain 'P' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'P' and resid 954 through 957 removed outlier: 6.465A pdb=" N ILE P 7 " --> pdb=" O VAL P 760 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLU P 762 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 6.191A 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: 10.015A pdb=" N GLU P1357 " --> pdb=" O LYS P 31 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS P 33 " --> pdb=" O GLU P1357 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ARG P1359 " --> pdb=" O LYS P 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU P 35 " --> pdb=" O ARG P1359 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP P1361 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER P1202 " --> pdb=" O LEU P1214 " (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 1049 through 1051 Processing sheet with id=AA5, first strand: chain 'P' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'P' and resid 1156 through 1167 removed outlier: 3.523A pdb=" N TYR P1141 " --> pdb=" O ILE P1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 1324 through 1325 412 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 4.37 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: 2580 1.34 - 1.46: 1914 1.46 - 1.58: 5028 1.58 - 1.70: 95 1.70 - 1.82: 31 Bond restraints: 9648 Sorted by residual: bond pdb=" CB ILE P 322 " pdb=" CG2 ILE P 322 " ideal model delta sigma weight residual 1.521 1.600 -0.079 3.30e-02 9.18e+02 5.78e+00 bond pdb=" CB ILE P1281 " pdb=" CG2 ILE P1281 " ideal model delta sigma weight residual 1.521 1.581 -0.060 3.30e-02 9.18e+02 3.36e+00 bond pdb=" CB ILE P 950 " pdb=" CG2 ILE P 950 " ideal model delta sigma weight residual 1.521 1.581 -0.060 3.30e-02 9.18e+02 3.32e+00 bond pdb=" C VAL P 842 " pdb=" N PRO P 843 " ideal model delta sigma weight residual 1.332 1.355 -0.024 1.33e-02 5.65e+03 3.18e+00 bond pdb=" CB ILE P1196 " pdb=" CG2 ILE P1196 " ideal model delta sigma weight residual 1.521 1.578 -0.057 3.30e-02 9.18e+02 2.95e+00 ... (remaining 9643 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.21: 226 104.21 - 111.66: 4149 111.66 - 119.11: 3980 119.11 - 126.56: 4618 126.56 - 134.01: 226 Bond angle restraints: 13199 Sorted by residual: angle pdb=" CA GLN P 402 " pdb=" CB GLN P 402 " pdb=" CG GLN P 402 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N VAL P1280 " pdb=" CA VAL P1280 " pdb=" C VAL P1280 " ideal model delta sigma weight residual 109.34 117.35 -8.01 2.08e+00 2.31e-01 1.48e+01 angle pdb=" CA GLU P 427 " pdb=" CB GLU P 427 " pdb=" CG GLU P 427 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" C TYR P1326 " pdb=" N PHE P1327 " pdb=" CA PHE P1327 " ideal model delta sigma weight residual 121.54 128.42 -6.88 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C THR P 769 " pdb=" N THR P 770 " pdb=" CA THR P 770 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 ... (remaining 13194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.22: 5502 20.22 - 40.44: 299 40.44 - 60.65: 84 60.65 - 80.87: 43 80.87 - 101.09: 4 Dihedral angle restraints: 5932 sinusoidal: 2895 harmonic: 3037 Sorted by residual: dihedral pdb=" CA PHE P1327 " pdb=" C PHE P1327 " pdb=" N ASP P1328 " pdb=" CA ASP P1328 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" C GLN P 402 " pdb=" N GLN P 402 " pdb=" CA GLN P 402 " pdb=" CB GLN P 402 " ideal model delta harmonic sigma weight residual -122.60 -131.10 8.50 0 2.50e+00 1.60e-01 1.15e+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 -88.34 58.34 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1018 0.043 - 0.085: 364 0.085 - 0.128: 90 0.128 - 0.170: 29 0.170 - 0.213: 5 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CA GLN P 402 " pdb=" N GLN P 402 " pdb=" C GLN P 402 " pdb=" CB GLN P 402 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+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 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE P 950 " pdb=" N ILE P 950 " pdb=" C ILE P 950 " pdb=" CB ILE P 950 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 1503 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P1270 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ILE P1270 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE P1270 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU P1271 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 32 " 0.026 2.00e-02 2.50e+03 2.19e-02 1.31e+01 pdb=" N9 A R 32 " -0.059 2.00e-02 2.50e+03 pdb=" C8 A R 32 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A R 32 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A R 32 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" N1 A R 32 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A R 32 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A R 32 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A R 32 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 275 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LEU P 275 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU P 275 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP P 276 " 0.021 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 838 2.75 - 3.29: 9239 3.29 - 3.82: 15062 3.82 - 4.36: 18525 4.36 - 4.90: 30526 Nonbonded interactions: 74190 Sorted by model distance: nonbonded pdb=" O GLN P 817 " pdb=" OH TYR P 882 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU P 762 " pdb=" OG SER P 960 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASN P 199 " pdb=" NH1 ARG P 783 " model vdw 2.243 2.520 nonbonded pdb=" OG SER P 867 " pdb=" OD1 ASN P 869 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASP P1267 " pdb=" OH TYR P1294 " model vdw 2.256 2.440 ... (remaining 74185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.670 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: 3.940 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.080 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 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 : 0.006 0.079 9648 Z= 0.430 Angle : 1.037 9.824 13199 Z= 0.564 Chirality : 0.049 0.213 1506 Planarity : 0.006 0.038 1517 Dihedral : 14.453 101.089 3968 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.23), residues: 1025 helix: -0.83 (0.20), residues: 508 sheet: -0.90 (0.43), residues: 127 loop : -0.96 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 883 HIS 0.016 0.002 HIS P 137 PHE 0.032 0.002 PHE P1313 TYR 0.015 0.002 TYR P 132 ARG 0.016 0.001 ARG P1060 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 269 average time/residue: 0.2961 time to fit residues: 102.0750 Evaluate side-chains 160 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1332 time to fit residues: 1.8251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.0270 chunk 27 optimal weight: 0.0000 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 0.0010 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 overall best weight: 0.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 716 GLN ** P 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1241 HIS ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9648 Z= 0.170 Angle : 0.577 6.811 13199 Z= 0.307 Chirality : 0.039 0.222 1506 Planarity : 0.004 0.034 1517 Dihedral : 14.309 94.421 1786 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.52 % Allowed : 12.81 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1025 helix: 0.70 (0.22), residues: 504 sheet: -0.61 (0.43), residues: 129 loop : -0.60 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 883 HIS 0.008 0.001 HIS P 420 PHE 0.043 0.002 PHE P 916 TYR 0.018 0.001 TYR P1001 ARG 0.005 0.001 ARG P 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 183 average time/residue: 0.2747 time to fit residues: 66.2518 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0980 time to fit residues: 3.0093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9648 Z= 0.220 Angle : 0.593 10.277 13199 Z= 0.313 Chirality : 0.040 0.165 1506 Planarity : 0.004 0.039 1517 Dihedral : 14.370 95.512 1786 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.17 % Allowed : 15.42 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1025 helix: 0.90 (0.23), residues: 510 sheet: -0.22 (0.48), residues: 108 loop : -0.52 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 883 HIS 0.010 0.002 HIS P 415 PHE 0.034 0.002 PHE P 916 TYR 0.017 0.002 TYR P 81 ARG 0.011 0.001 ARG P1171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 162 average time/residue: 0.2652 time to fit residues: 57.0198 Evaluate side-chains 136 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0911 time to fit residues: 2.9598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 228 GLN ** P 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9648 Z= 0.171 Angle : 0.557 7.453 13199 Z= 0.292 Chirality : 0.038 0.161 1506 Planarity : 0.004 0.040 1517 Dihedral : 14.336 95.523 1786 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.74 % Allowed : 16.29 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1025 helix: 0.94 (0.22), residues: 517 sheet: -0.12 (0.48), residues: 108 loop : -0.51 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P1074 HIS 0.005 0.001 HIS P 420 PHE 0.041 0.002 PHE P 916 TYR 0.017 0.001 TYR P 286 ARG 0.009 0.001 ARG P1171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 152 average time/residue: 0.2658 time to fit residues: 53.4473 Evaluate side-chains 142 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0904 time to fit residues: 3.4551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 295 ASN ** P 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1044 ASN P1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 9648 Z= 0.621 Angle : 0.972 18.295 13199 Z= 0.515 Chirality : 0.052 0.187 1506 Planarity : 0.007 0.076 1517 Dihedral : 15.138 102.679 1786 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 28.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.37 % Allowed : 16.18 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.24), residues: 1025 helix: -0.60 (0.20), residues: 523 sheet: -0.35 (0.49), residues: 99 loop : -1.21 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P1074 HIS 0.012 0.003 HIS P 412 PHE 0.043 0.004 PHE P 916 TYR 0.024 0.003 TYR P 823 ARG 0.012 0.001 ARG P 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 174 average time/residue: 0.2767 time to fit residues: 63.7713 Evaluate side-chains 143 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0939 time to fit residues: 4.6111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 407 ASN P 758 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9648 Z= 0.213 Angle : 0.634 8.170 13199 Z= 0.333 Chirality : 0.041 0.174 1506 Planarity : 0.004 0.046 1517 Dihedral : 14.701 98.397 1786 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.52 % Allowed : 18.57 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1025 helix: 0.17 (0.22), residues: 523 sheet: -0.13 (0.49), residues: 97 loop : -0.99 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP P 18 HIS 0.006 0.001 HIS P 420 PHE 0.040 0.002 PHE P 916 TYR 0.036 0.002 TYR P 981 ARG 0.006 0.001 ARG P 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 153 average time/residue: 0.3179 time to fit residues: 64.7872 Evaluate side-chains 140 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0908 time to fit residues: 2.4090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 64 optimal weight: 0.0070 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 295 ASN P 758 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9648 Z= 0.192 Angle : 0.622 8.362 13199 Z= 0.321 Chirality : 0.040 0.176 1506 Planarity : 0.004 0.047 1517 Dihedral : 14.582 98.633 1786 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.30 % Allowed : 19.98 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1025 helix: 0.54 (0.23), residues: 523 sheet: 0.04 (0.50), residues: 97 loop : -0.89 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 18 HIS 0.007 0.001 HIS P 420 PHE 0.036 0.002 PHE P 916 TYR 0.021 0.001 TYR P 362 ARG 0.011 0.001 ARG P1171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 150 average time/residue: 0.2659 time to fit residues: 53.2933 Evaluate side-chains 136 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1906 time to fit residues: 2.7989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9648 Z= 0.239 Angle : 0.653 9.669 13199 Z= 0.337 Chirality : 0.041 0.201 1506 Planarity : 0.004 0.062 1517 Dihedral : 14.589 100.275 1786 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.30 % Allowed : 19.54 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1025 helix: 0.55 (0.23), residues: 526 sheet: 0.05 (0.50), residues: 97 loop : -0.97 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP P 18 HIS 0.005 0.001 HIS P 167 PHE 0.049 0.002 PHE P 916 TYR 0.056 0.002 TYR P1237 ARG 0.007 0.001 ARG P 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 141 average time/residue: 0.2952 time to fit residues: 55.9142 Evaluate side-chains 137 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0925 time to fit residues: 2.0060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9648 Z= 0.190 Angle : 0.658 17.253 13199 Z= 0.332 Chirality : 0.040 0.193 1506 Planarity : 0.005 0.114 1517 Dihedral : 14.526 99.234 1786 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.54 % Allowed : 20.63 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1025 helix: 0.59 (0.23), residues: 527 sheet: -0.03 (0.49), residues: 99 loop : -0.94 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP P 18 HIS 0.007 0.001 HIS P 420 PHE 0.049 0.002 PHE P 916 TYR 0.043 0.002 TYR P1237 ARG 0.017 0.001 ARG P 780 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 140 average time/residue: 0.2805 time to fit residues: 52.3884 Evaluate side-chains 135 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1259 time to fit residues: 2.3966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 818 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9648 Z= 0.193 Angle : 0.660 15.775 13199 Z= 0.336 Chirality : 0.040 0.195 1506 Planarity : 0.006 0.169 1517 Dihedral : 14.472 99.489 1786 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 21.50 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1025 helix: 0.62 (0.23), residues: 527 sheet: -0.01 (0.49), residues: 99 loop : -0.87 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP P 18 HIS 0.006 0.001 HIS P 420 PHE 0.048 0.002 PHE P 916 TYR 0.039 0.002 TYR P1237 ARG 0.027 0.001 ARG P 780 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2653 time to fit residues: 51.1090 Evaluate side-chains 135 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1317 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 = 0.4375 r_free = 0.4375 target = 0.148308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.125383 restraints weight = 27149.912| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 3.45 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9648 Z= 0.180 Angle : 0.655 15.514 13199 Z= 0.334 Chirality : 0.040 0.191 1506 Planarity : 0.006 0.157 1517 Dihedral : 14.428 99.350 1786 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.33 % Allowed : 21.17 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1025 helix: 0.63 (0.23), residues: 529 sheet: 0.04 (0.49), residues: 99 loop : -0.80 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP P 18 HIS 0.006 0.001 HIS P 420 PHE 0.049 0.002 PHE P 916 TYR 0.035 0.002 TYR P1237 ARG 0.028 0.001 ARG P 780 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.85 seconds wall clock time: 42 minutes 56.80 seconds (2576.80 seconds total)