Starting phenix.real_space_refine on Thu Mar 14 17:50:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/03_2024/7s37_24818.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/03_2024/7s37_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_24818/03_2024/7s37_24818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/03_2024/7s37_24818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/03_2024/7s37_24818.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s37_24818/03_2024/7s37_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-dev-5265/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: 5.54, 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: 3.77 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: 3.48 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: 3.68 Time building geometry restraints manager: 4.07 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: 5515 20.22 - 40.44: 307 40.44 - 60.65: 99 60.65 - 80.87: 43 80.87 - 101.09: 4 Dihedral angle restraints: 5968 sinusoidal: 2931 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 5965 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.960 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.870 Find NCS groups from input model: 0.200 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.820 ------------------------------------------------------------------------------- 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 : 14.849 101.089 4004 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 : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7270 (pt0) REVERT: P 72 TYR cc_start: 0.7405 (t80) cc_final: 0.7188 (t80) REVERT: P 75 ARG cc_start: 0.8450 (mtt180) cc_final: 0.7938 (mmt90) REVERT: P 76 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8164 (mmmt) REVERT: P 77 ASN cc_start: 0.8123 (t0) cc_final: 0.7854 (t0) REVERT: P 163 LYS cc_start: 0.8136 (tttt) cc_final: 0.7652 (ttpt) REVERT: P 222 LEU cc_start: 0.8416 (tp) cc_final: 0.8196 (tt) REVERT: P 286 TYR cc_start: 0.7743 (m-80) cc_final: 0.7405 (m-10) REVERT: P 394 ASN cc_start: 0.7609 (t0) cc_final: 0.7235 (p0) REVERT: P 742 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7186 (mmmt) REVERT: P 751 MET cc_start: 0.6756 (mmt) cc_final: 0.6061 (mmt) REVERT: P 763 MET cc_start: 0.8020 (mmt) cc_final: 0.7818 (mmm) REVERT: P 937 SER cc_start: 0.6958 (t) cc_final: 0.6667 (m) outliers start: 1 outliers final: 1 residues processed: 269 average time/residue: 0.2876 time to fit residues: 99.2565 Evaluate side-chains 166 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.0000 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 0.0010 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 224 ASN ** P 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6369 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9648 Z= 0.182 Angle : 0.589 7.031 13199 Z= 0.314 Chirality : 0.039 0.218 1506 Planarity : 0.003 0.030 1517 Dihedral : 15.142 95.652 1824 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.63 % Allowed : 12.70 % 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: 0.01 (0.25), residues: 1025 helix: 0.71 (0.23), residues: 504 sheet: -0.60 (0.43), residues: 129 loop : -0.57 (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 0.038 0.002 PHE P 916 TYR 0.019 0.001 TYR P1001 ARG 0.008 0.001 ARG P 400 *********************** 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: 15 poor density : 179 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6696 (mtm180) REVERT: P 75 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8104 (mmt90) REVERT: P 76 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8062 (mmmt) REVERT: P 77 ASN cc_start: 0.8031 (t0) cc_final: 0.7584 (t0) REVERT: P 163 LYS cc_start: 0.8096 (tttt) cc_final: 0.7795 (ttpt) REVERT: P 170 ILE cc_start: 0.7141 (mm) cc_final: 0.6895 (pt) REVERT: P 285 GLN cc_start: 0.8359 (pt0) cc_final: 0.7850 (pm20) REVERT: P 286 TYR cc_start: 0.7723 (m-80) cc_final: 0.7404 (m-10) REVERT: P 380 LEU cc_start: 0.8037 (mt) cc_final: 0.7773 (mt) REVERT: P 394 ASN cc_start: 0.7481 (t0) cc_final: 0.7218 (p0) REVERT: P 418 GLU cc_start: 0.8005 (mp0) cc_final: 0.7780 (mp0) REVERT: P 740 THR cc_start: 0.7969 (m) cc_final: 0.7644 (p) REVERT: P 742 LYS cc_start: 0.7618 (mtmt) cc_final: 0.7149 (mmmt) REVERT: P 763 MET cc_start: 0.7796 (mmt) cc_final: 0.7511 (mmm) REVERT: P 926 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7041 (tp-100) REVERT: P 937 SER cc_start: 0.6906 (t) cc_final: 0.6655 (m) REVERT: P 970 PHE cc_start: 0.6750 (m-80) cc_final: 0.5773 (m-80) REVERT: P 981 TYR cc_start: 0.6877 (m-10) cc_final: 0.6664 (m-10) outliers start: 15 outliers final: 10 residues processed: 185 average time/residue: 0.2638 time to fit residues: 64.4848 Evaluate side-chains 158 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1364 GLN 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: 0.4980 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 228 GLN P1044 ASN P1221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9648 Z= 0.266 Angle : 0.655 13.679 13199 Z= 0.341 Chirality : 0.041 0.177 1506 Planarity : 0.004 0.041 1517 Dihedral : 15.200 96.976 1822 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.93 % Allowed : 14.98 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.26), residues: 1025 helix: 0.74 (0.22), residues: 517 sheet: -0.22 (0.48), residues: 108 loop : -0.61 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 883 HIS 0.006 0.002 HIS P 412 PHE 0.031 0.002 PHE P 916 TYR 0.019 0.002 TYR P 823 ARG 0.014 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 189 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 76 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8180 (mmmt) REVERT: P 77 ASN cc_start: 0.8023 (t0) cc_final: 0.7741 (t0) REVERT: P 163 LYS cc_start: 0.8189 (tttt) cc_final: 0.7805 (ttpt) REVERT: P 257 ASP cc_start: 0.7127 (t0) cc_final: 0.6894 (t0) REVERT: P 286 TYR cc_start: 0.7829 (m-80) cc_final: 0.7609 (m-10) REVERT: P 321 MET cc_start: 0.6839 (mmp) cc_final: 0.6545 (mmp) REVERT: P 380 LEU cc_start: 0.8032 (mt) cc_final: 0.7830 (mt) REVERT: P 394 ASN cc_start: 0.7662 (t0) cc_final: 0.7277 (p0) REVERT: P 418 GLU cc_start: 0.7967 (mp0) cc_final: 0.7696 (mm-30) REVERT: P 740 THR cc_start: 0.8013 (m) cc_final: 0.7630 (p) REVERT: P 742 LYS cc_start: 0.7613 (mtmt) cc_final: 0.7182 (mmtt) REVERT: P 749 LYS cc_start: 0.7926 (tttt) cc_final: 0.7630 (tttm) REVERT: P 763 MET cc_start: 0.7773 (mmt) cc_final: 0.7417 (mmm) REVERT: P 926 GLN cc_start: 0.7640 (tp-100) cc_final: 0.7077 (tp-100) REVERT: P 927 ILE cc_start: 0.8690 (tp) cc_final: 0.8229 (pt) REVERT: P 937 SER cc_start: 0.7192 (t) cc_final: 0.6957 (m) REVERT: P 1021 MET cc_start: 0.4445 (mmt) cc_final: 0.4159 (mmt) REVERT: P 1089 MET cc_start: 0.5597 (mtp) cc_final: 0.5368 (mtp) outliers start: 27 outliers final: 20 residues processed: 179 average time/residue: 0.2673 time to fit residues: 63.5125 Evaluate side-chains 164 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1087 LEU Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1179 ILE Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1270 ILE Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.0770 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9648 Z= 0.173 Angle : 0.562 10.752 13199 Z= 0.293 Chirality : 0.038 0.142 1506 Planarity : 0.004 0.044 1517 Dihedral : 15.120 95.927 1822 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.17 % Allowed : 16.83 % Favored : 81.00 % 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: 0.33 (0.26), residues: 1025 helix: 0.98 (0.23), residues: 512 sheet: -0.22 (0.47), residues: 108 loop : -0.54 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P1074 HIS 0.004 0.001 HIS P1297 PHE 0.042 0.002 PHE P 916 TYR 0.016 0.001 TYR P 72 ARG 0.009 0.001 ARG P1335 *********************** 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 171 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 76 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8141 (mmmt) REVERT: P 77 ASN cc_start: 0.7958 (t0) cc_final: 0.7732 (t0) REVERT: P 163 LYS cc_start: 0.8054 (tttt) cc_final: 0.7749 (ttpt) REVERT: P 257 ASP cc_start: 0.7210 (t0) cc_final: 0.6875 (t0) REVERT: P 321 MET cc_start: 0.6851 (mmp) cc_final: 0.6618 (mmp) REVERT: P 380 LEU cc_start: 0.8038 (mt) cc_final: 0.7836 (mt) REVERT: P 394 ASN cc_start: 0.7749 (t0) cc_final: 0.7373 (p0) REVERT: P 418 GLU cc_start: 0.7988 (mp0) cc_final: 0.7743 (mm-30) REVERT: P 740 THR cc_start: 0.8091 (m) cc_final: 0.7732 (p) REVERT: P 742 LYS cc_start: 0.7602 (mtmt) cc_final: 0.7153 (mmmt) REVERT: P 749 LYS cc_start: 0.7860 (tttt) cc_final: 0.7613 (tttm) REVERT: P 763 MET cc_start: 0.7818 (mmt) cc_final: 0.7418 (mmm) REVERT: P 926 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7083 (tp-100) REVERT: P 927 ILE cc_start: 0.8638 (tp) cc_final: 0.8197 (pt) REVERT: P 937 SER cc_start: 0.7227 (t) cc_final: 0.7009 (m) REVERT: P 967 ARG cc_start: 0.6724 (mtt180) cc_final: 0.6436 (mtt180) REVERT: P 1060 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6854 (mtp-110) REVERT: P 1089 MET cc_start: 0.5583 (mtp) cc_final: 0.5224 (mtp) outliers start: 20 outliers final: 12 residues processed: 163 average time/residue: 0.2705 time to fit residues: 57.9089 Evaluate side-chains 155 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.0270 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 71 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9648 Z= 0.146 Angle : 0.541 9.645 13199 Z= 0.278 Chirality : 0.037 0.145 1506 Planarity : 0.003 0.042 1517 Dihedral : 15.072 96.522 1822 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.37 % Allowed : 16.50 % Favored : 80.13 % 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: 0.48 (0.26), residues: 1025 helix: 1.19 (0.23), residues: 511 sheet: -0.02 (0.47), residues: 108 loop : -0.65 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P1074 HIS 0.005 0.001 HIS P1297 PHE 0.043 0.002 PHE P 916 TYR 0.019 0.001 TYR P 286 ARG 0.005 0.000 ARG P1333 *********************** 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 184 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 76 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8130 (mmmt) REVERT: P 77 ASN cc_start: 0.7907 (t0) cc_final: 0.7672 (t0) REVERT: P 163 LYS cc_start: 0.8051 (tttt) cc_final: 0.7848 (ttpt) REVERT: P 285 GLN cc_start: 0.8663 (pt0) cc_final: 0.8382 (pm20) REVERT: P 286 TYR cc_start: 0.7804 (m-10) cc_final: 0.7476 (m-10) REVERT: P 321 MET cc_start: 0.6895 (mmp) cc_final: 0.6621 (mmp) REVERT: P 354 GLN cc_start: 0.7656 (mt0) cc_final: 0.7220 (tm-30) REVERT: P 394 ASN cc_start: 0.7697 (t0) cc_final: 0.7365 (p0) REVERT: P 418 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: P 740 THR cc_start: 0.8146 (m) cc_final: 0.7795 (p) REVERT: P 742 LYS cc_start: 0.7626 (mtmt) cc_final: 0.7145 (mmmt) REVERT: P 745 ASP cc_start: 0.7633 (m-30) cc_final: 0.7392 (t0) REVERT: P 908 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7209 (mp) REVERT: P 926 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7057 (tp-100) REVERT: P 927 ILE cc_start: 0.8595 (tp) cc_final: 0.8169 (pt) REVERT: P 1060 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6761 (mtp-110) REVERT: P 1089 MET cc_start: 0.5729 (mtp) cc_final: 0.5333 (mtp) REVERT: P 1164 LEU cc_start: 0.7018 (pt) cc_final: 0.6739 (pt) outliers start: 31 outliers final: 16 residues processed: 174 average time/residue: 0.2528 time to fit residues: 58.5584 Evaluate side-chains 163 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 944 ASP Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9648 Z= 0.179 Angle : 0.555 8.296 13199 Z= 0.288 Chirality : 0.038 0.143 1506 Planarity : 0.004 0.045 1517 Dihedral : 15.065 98.844 1822 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.47 % Allowed : 16.50 % Favored : 80.02 % 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: 0.47 (0.26), residues: 1025 helix: 1.13 (0.23), residues: 515 sheet: 0.02 (0.47), residues: 109 loop : -0.60 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P1074 HIS 0.004 0.001 HIS P1297 PHE 0.041 0.002 PHE P 916 TYR 0.037 0.002 TYR P1237 ARG 0.011 0.001 ARG P1171 *********************** 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 188 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 1.005 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 76 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8161 (mmmt) REVERT: P 77 ASN cc_start: 0.7975 (t0) cc_final: 0.7748 (t0) REVERT: P 163 LYS cc_start: 0.8059 (tttt) cc_final: 0.7839 (ttpt) REVERT: P 285 GLN cc_start: 0.8622 (pt0) cc_final: 0.8381 (pm20) REVERT: P 286 TYR cc_start: 0.7804 (m-10) cc_final: 0.7463 (m-10) REVERT: P 321 MET cc_start: 0.6980 (mmp) cc_final: 0.6747 (mmp) REVERT: P 354 GLN cc_start: 0.7618 (mt0) cc_final: 0.7253 (tm-30) REVERT: P 394 ASN cc_start: 0.7784 (t0) cc_final: 0.7522 (p0) REVERT: P 418 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: P 722 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7945 (mt-10) REVERT: P 740 THR cc_start: 0.8170 (m) cc_final: 0.7859 (p) REVERT: P 742 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7122 (mmmt) REVERT: P 745 ASP cc_start: 0.7688 (m-30) cc_final: 0.7443 (t0) REVERT: P 908 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7289 (mp) REVERT: P 926 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7177 (tp-100) REVERT: P 927 ILE cc_start: 0.8656 (tp) cc_final: 0.8228 (pt) REVERT: P 1060 ARG cc_start: 0.7023 (mmm160) cc_final: 0.6794 (mtp-110) REVERT: P 1089 MET cc_start: 0.5708 (mtp) cc_final: 0.5255 (mtp) REVERT: P 1164 LEU cc_start: 0.7133 (pt) cc_final: 0.6904 (pt) outliers start: 32 outliers final: 24 residues processed: 174 average time/residue: 0.2636 time to fit residues: 60.9179 Evaluate side-chains 165 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 831 ASN Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 944 ASP Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1270 ILE Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.5472 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= 0.223 Angle : 0.590 8.623 13199 Z= 0.310 Chirality : 0.039 0.153 1506 Planarity : 0.004 0.043 1517 Dihedral : 15.121 100.572 1822 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.91 % Allowed : 17.05 % Favored : 79.04 % 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: 0.25 (0.26), residues: 1025 helix: 0.97 (0.23), residues: 521 sheet: -0.15 (0.46), residues: 109 loop : -0.74 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 18 HIS 0.005 0.001 HIS P 167 PHE 0.044 0.002 PHE P 916 TYR 0.037 0.002 TYR P1237 ARG 0.004 0.001 ARG P1333 *********************** 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 187 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 75 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8045 (mtp85) REVERT: P 76 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8201 (mmmt) REVERT: P 77 ASN cc_start: 0.7997 (t0) cc_final: 0.7765 (t0) REVERT: P 163 LYS cc_start: 0.8120 (tttt) cc_final: 0.7730 (ttpt) REVERT: P 285 GLN cc_start: 0.8698 (pt0) cc_final: 0.8375 (pm20) REVERT: P 286 TYR cc_start: 0.7960 (m-10) cc_final: 0.7571 (m-10) REVERT: P 354 GLN cc_start: 0.7735 (mt0) cc_final: 0.7377 (tm-30) REVERT: P 394 ASN cc_start: 0.7848 (t0) cc_final: 0.7435 (p0) REVERT: P 722 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8022 (mt-10) REVERT: P 740 THR cc_start: 0.8137 (m) cc_final: 0.7784 (p) REVERT: P 742 LYS cc_start: 0.7436 (mtmt) cc_final: 0.7033 (mmtt) REVERT: P 745 ASP cc_start: 0.7720 (m-30) cc_final: 0.7468 (t0) REVERT: P 908 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7385 (mt) REVERT: P 926 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7356 (tp-100) REVERT: P 927 ILE cc_start: 0.8713 (tp) cc_final: 0.8300 (pt) REVERT: P 1060 ARG cc_start: 0.7059 (mmm160) cc_final: 0.6849 (mtp-110) outliers start: 36 outliers final: 24 residues processed: 174 average time/residue: 0.2588 time to fit residues: 60.5016 Evaluate side-chains 165 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 269 ASP Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 831 ASN Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 944 ASP Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1179 ILE Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1270 ILE Chi-restraints excluded: chain P residue 1314 THR Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9648 Z= 0.180 Angle : 0.580 8.196 13199 Z= 0.300 Chirality : 0.038 0.182 1506 Planarity : 0.004 0.043 1517 Dihedral : 15.093 99.808 1822 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.50 % Allowed : 18.02 % Favored : 79.48 % 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: 0.33 (0.26), residues: 1025 helix: 1.05 (0.23), residues: 514 sheet: -0.08 (0.46), residues: 109 loop : -0.71 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P1074 HIS 0.005 0.001 HIS P1297 PHE 0.052 0.002 PHE P 916 TYR 0.026 0.002 TYR P1237 ARG 0.005 0.000 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 170 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.087 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 4 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7920 (ttmm) REVERT: P 75 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8029 (mtp85) REVERT: P 76 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8185 (mmmt) REVERT: P 77 ASN cc_start: 0.7951 (t0) cc_final: 0.7732 (t0) REVERT: P 163 LYS cc_start: 0.8024 (tttt) cc_final: 0.7630 (ttpt) REVERT: P 286 TYR cc_start: 0.7935 (m-10) cc_final: 0.7636 (m-10) REVERT: P 354 GLN cc_start: 0.7663 (mt0) cc_final: 0.7405 (tm-30) REVERT: P 394 ASN cc_start: 0.7877 (t0) cc_final: 0.7578 (p0) REVERT: P 722 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8061 (mt-10) REVERT: P 740 THR cc_start: 0.8124 (m) cc_final: 0.7774 (p) REVERT: P 742 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7143 (mmtt) REVERT: P 745 ASP cc_start: 0.7689 (m-30) cc_final: 0.7444 (t0) REVERT: P 908 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7365 (mt) REVERT: P 926 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7307 (tp-100) REVERT: P 927 ILE cc_start: 0.8678 (tp) cc_final: 0.8269 (pt) REVERT: P 967 ARG cc_start: 0.6995 (ppt170) cc_final: 0.6784 (ppt170) REVERT: P 1060 ARG cc_start: 0.7074 (mmm160) cc_final: 0.6868 (mtp-110) REVERT: P 1089 MET cc_start: 0.5788 (mtp) cc_final: 0.5484 (mtp) outliers start: 23 outliers final: 19 residues processed: 162 average time/residue: 0.2799 time to fit residues: 60.3634 Evaluate side-chains 166 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 269 ASP Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 831 ASN Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 944 ASP Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 716 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9648 Z= 0.249 Angle : 0.640 9.911 13199 Z= 0.331 Chirality : 0.040 0.193 1506 Planarity : 0.004 0.045 1517 Dihedral : 15.173 100.855 1822 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.82 % Allowed : 18.13 % Favored : 79.04 % 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: 0.07 (0.26), residues: 1025 helix: 0.78 (0.23), residues: 525 sheet: -0.16 (0.46), residues: 109 loop : -0.80 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 18 HIS 0.006 0.002 HIS P 167 PHE 0.052 0.002 PHE P 916 TYR 0.027 0.002 TYR P1237 ARG 0.005 0.001 ARG P 139 *********************** 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 176 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.960 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 4 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8030 (ttmm) REVERT: P 75 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8125 (mtp85) REVERT: P 76 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8152 (mmmt) REVERT: P 77 ASN cc_start: 0.8043 (t0) cc_final: 0.7795 (t0) REVERT: P 163 LYS cc_start: 0.8047 (tttt) cc_final: 0.7694 (ttpt) REVERT: P 286 TYR cc_start: 0.7947 (m-80) cc_final: 0.7660 (m-10) REVERT: P 354 GLN cc_start: 0.7738 (mt0) cc_final: 0.7460 (tm-30) REVERT: P 383 MET cc_start: 0.6676 (ptp) cc_final: 0.5897 (ptm) REVERT: P 394 ASN cc_start: 0.7853 (t0) cc_final: 0.7552 (p0) REVERT: P 722 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8027 (mt-10) REVERT: P 740 THR cc_start: 0.8139 (m) cc_final: 0.7795 (p) REVERT: P 742 LYS cc_start: 0.7521 (mtmt) cc_final: 0.7133 (mmtt) REVERT: P 745 ASP cc_start: 0.7729 (m-30) cc_final: 0.7485 (t0) REVERT: P 926 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7329 (tp-100) REVERT: P 927 ILE cc_start: 0.8721 (tp) cc_final: 0.8304 (pt) REVERT: P 944 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.5911 (p0) REVERT: P 1060 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6849 (mtp-110) REVERT: P 1089 MET cc_start: 0.5778 (mtp) cc_final: 0.5443 (mtp) REVERT: P 1356 TYR cc_start: 0.7553 (m-10) cc_final: 0.7321 (m-10) outliers start: 26 outliers final: 21 residues processed: 166 average time/residue: 0.2673 time to fit residues: 58.7573 Evaluate side-chains 166 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 269 ASP Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 831 ASN Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 944 ASP Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1270 ILE Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9648 Z= 0.167 Angle : 0.622 16.303 13199 Z= 0.312 Chirality : 0.039 0.191 1506 Planarity : 0.004 0.074 1517 Dihedral : 15.094 99.089 1822 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 20.52 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.26), residues: 1025 helix: 0.95 (0.23), residues: 511 sheet: -0.12 (0.46), residues: 111 loop : -0.71 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P1074 HIS 0.006 0.001 HIS P1297 PHE 0.053 0.002 PHE P 916 TYR 0.028 0.001 TYR P1237 ARG 0.016 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 170 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 4 LYS cc_start: 0.8270 (ttmt) cc_final: 0.8018 (ttmm) REVERT: P 75 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8036 (mtp85) REVERT: P 76 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8134 (mmmt) REVERT: P 77 ASN cc_start: 0.7871 (t0) cc_final: 0.7640 (t0) REVERT: P 163 LYS cc_start: 0.7994 (tttt) cc_final: 0.7639 (ttpt) REVERT: P 285 GLN cc_start: 0.8644 (pt0) cc_final: 0.8235 (pm20) REVERT: P 286 TYR cc_start: 0.7887 (m-80) cc_final: 0.7372 (m-10) REVERT: P 354 GLN cc_start: 0.7718 (mt0) cc_final: 0.7470 (tm-30) REVERT: P 383 MET cc_start: 0.6663 (ptp) cc_final: 0.5846 (ptm) REVERT: P 384 ASP cc_start: 0.8761 (m-30) cc_final: 0.8347 (t0) REVERT: P 394 ASN cc_start: 0.7848 (t0) cc_final: 0.7547 (p0) REVERT: P 722 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7761 (mt-10) REVERT: P 740 THR cc_start: 0.8126 (m) cc_final: 0.7782 (p) REVERT: P 742 LYS cc_start: 0.7513 (mtmt) cc_final: 0.7142 (mmtt) REVERT: P 780 ARG cc_start: 0.6401 (mtm180) cc_final: 0.6119 (ptm160) REVERT: P 926 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7354 (tp-100) REVERT: P 927 ILE cc_start: 0.8655 (tp) cc_final: 0.8254 (pt) REVERT: P 1060 ARG cc_start: 0.7076 (mmm160) cc_final: 0.6855 (mtp-110) REVERT: P 1356 TYR cc_start: 0.7525 (m-10) cc_final: 0.7312 (m-10) outliers start: 17 outliers final: 15 residues processed: 164 average time/residue: 0.2574 time to fit residues: 56.3155 Evaluate side-chains 158 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 269 ASP Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 831 ASN Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 944 ASP Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 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 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.147716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.125789 restraints weight = 27304.462| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.48 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9648 Z= 0.189 Angle : 0.639 15.402 13199 Z= 0.322 Chirality : 0.039 0.190 1506 Planarity : 0.004 0.071 1517 Dihedral : 15.078 99.790 1822 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 20.30 % Favored : 77.52 % 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: 0.20 (0.26), residues: 1025 helix: 0.92 (0.23), residues: 510 sheet: -0.12 (0.45), residues: 111 loop : -0.71 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P1074 HIS 0.005 0.001 HIS P1297 PHE 0.055 0.002 PHE P 916 TYR 0.026 0.002 TYR P1237 ARG 0.008 0.001 ARG P 780 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.80 seconds wall clock time: 41 minutes 6.08 seconds (2466.08 seconds total)