Starting phenix.real_space_refine on Wed Sep 25 22:35:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/09_2024/7si7_25139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/09_2024/7si7_25139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/09_2024/7si7_25139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/09_2024/7si7_25139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/09_2024/7si7_25139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/09_2024/7si7_25139.cif" } resolution = 3.49 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 1.000 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 38 5.16 5 C 3545 2.51 5 N 923 2.21 5 O 998 1.98 5 F 4 1.80 5 H 5777 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11287 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 11281 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 28, 'TRANS': 699} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.49, per 1000 atoms: 0.49 Number of scatterers: 11287 At special positions: 0 Unit cell: (71.4, 80.75, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 38 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 998 8.00 N 923 7.00 C 3545 6.00 H 5777 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 945.8 milliseconds 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1354 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 59.9% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 640 through 671 Proline residue: A 660 - end of helix Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'A' and resid 707 through 721 removed outlier: 4.355A pdb=" N PHE A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 752 Processing helix chain 'A' and resid 762 through 783 Processing helix chain 'A' and resid 787 through 796 removed outlier: 3.652A pdb=" N GLN A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 891 through 907 removed outlier: 3.523A pdb=" N LYS A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 943 removed outlier: 3.619A pdb=" N TYR A 920 " --> pdb=" O LYS A 916 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 944 through 951 Processing helix chain 'A' and resid 952 through 956 Processing helix chain 'A' and resid 959 through 980 removed outlier: 3.625A pdb=" N CYS A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.561A pdb=" N GLY A 985 " --> pdb=" O CYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1002 removed outlier: 4.263A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1016 removed outlier: 4.756A pdb=" N HIS A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1061 Processing helix chain 'A' and resid 1066 through 1080 Processing helix chain 'A' and resid 1105 through 1112 removed outlier: 3.602A pdb=" N VAL A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1164 Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1205 through 1218 removed outlier: 4.385A pdb=" N ALA A1209 " --> pdb=" O LYS A1205 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A1210 " --> pdb=" O GLN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1250 through 1264 Processing helix chain 'A' and resid 1277 through 1284 Processing helix chain 'A' and resid 1294 through 1301 Processing helix chain 'A' and resid 1310 through 1346 removed outlier: 4.218A pdb=" N VAL A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A1337 " --> pdb=" O PHE A1333 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN A1338 " --> pdb=" O ALA A1334 " (cutoff:3.500A) Proline residue: A1343 - end of helix Processing helix chain 'A' and resid 1357 through 1379 removed outlier: 4.089A pdb=" N GLY A1361 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER A1362 " --> pdb=" O PRO A1358 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET A1365 " --> pdb=" O GLY A1361 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A1379 " --> pdb=" O SER A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1382 No H-bonds generated for 'chain 'A' and resid 1380 through 1382' Processing helix chain 'A' and resid 1386 through 1394 Processing sheet with id=AA1, first strand: chain 'A' and resid 814 through 818 removed outlier: 4.091A pdb=" N ALA A 801 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE A 827 " --> pdb=" O VAL A 803 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 881 " --> pdb=" O ILE A 843 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP A 839 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 861 through 863 Processing sheet with id=AA3, first strand: chain 'A' and resid 1004 through 1006 removed outlier: 6.020A pdb=" N GLY A1287 " --> pdb=" O ILE A1303 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A1305 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA A1289 " --> pdb=" O LEU A1305 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1268 " --> pdb=" O VAL A1286 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A1288 " --> pdb=" O VAL A1268 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N MET A1270 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE A1290 " --> pdb=" O MET A1270 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A1020 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A1271 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET A1022 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A1222 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N PHE A1246 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A1224 " --> pdb=" O PHE A1246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1035 through 1041 removed outlier: 6.793A pdb=" N ALA A1199 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A1039 " --> pdb=" O MET A1197 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET A1197 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A1041 " --> pdb=" O CYS A1195 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N CYS A1195 " --> pdb=" O LEU A1041 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU A1194 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE A1190 " --> pdb=" O LEU A1194 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5768 1.03 - 1.23: 11 1.23 - 1.42: 2144 1.42 - 1.62: 3379 1.62 - 1.81: 71 Bond restraints: 11373 Sorted by residual: bond pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.684 1.784 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" F4 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.686 1.784 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" CA VAL A 922 " pdb=" CB VAL A 922 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.49e+00 ... (remaining 11368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.25: 20724 14.25 - 28.50: 4 28.50 - 42.75: 0 42.75 - 57.00: 0 57.00 - 71.25: 2 Bond angle restraints: 20730 Sorted by residual: angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 179.93 -71.25 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.97 -70.34 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 110.21 90.05 20.16 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.59 89.92 19.67 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.69 90.05 19.64 3.00e+00 1.11e-01 4.28e+01 ... (remaining 20725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4829 17.96 - 35.93: 345 35.93 - 53.89: 85 53.89 - 71.85: 18 71.85 - 89.82: 5 Dihedral angle restraints: 5282 sinusoidal: 2934 harmonic: 2348 Sorted by residual: dihedral pdb=" CB GLU A1013 " pdb=" CG GLU A1013 " pdb=" CD GLU A1013 " pdb=" OE1 GLU A1013 " ideal model delta sinusoidal sigma weight residual 0.00 -80.52 80.52 1 3.00e+01 1.11e-03 8.91e+00 dihedral pdb=" CA ARG A 824 " pdb=" CB ARG A 824 " pdb=" CG ARG A 824 " pdb=" CD ARG A 824 " ideal model delta sinusoidal sigma weight residual 180.00 130.04 49.96 3 1.50e+01 4.44e-03 8.84e+00 dihedral pdb=" CA LYS A 907 " pdb=" CB LYS A 907 " pdb=" CG LYS A 907 " pdb=" CD LYS A 907 " ideal model delta sinusoidal sigma weight residual -60.00 -108.26 48.26 3 1.50e+01 4.44e-03 8.61e+00 ... (remaining 5279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 607 0.027 - 0.055: 167 0.055 - 0.082: 89 0.082 - 0.109: 46 0.109 - 0.136: 28 Chirality restraints: 937 Sorted by residual: chirality pdb=" CA ILE A1154 " pdb=" N ILE A1154 " pdb=" C ILE A1154 " pdb=" CB ILE A1154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A1152 " pdb=" N VAL A1152 " pdb=" C VAL A1152 " pdb=" CB VAL A1152 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL A 686 " pdb=" N VAL A 686 " pdb=" C VAL A 686 " pdb=" CB VAL A 686 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 934 not shown) Planarity restraints: 1636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A1322 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C ARG A1322 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG A1322 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A1323 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1325 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C ARG A1325 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG A1325 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG A1326 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1323 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR A1323 " -0.023 2.00e-02 2.50e+03 pdb=" O THR A1323 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A1324 " 0.008 2.00e-02 2.50e+03 ... (remaining 1633 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 2648 2.31 - 2.88: 26841 2.88 - 3.46: 29180 3.46 - 4.03: 39314 4.03 - 4.60: 59511 Nonbonded interactions: 157494 Sorted by model distance: nonbonded pdb=" O ALA A1367 " pdb=" HG SER A1371 " model vdw 1.740 2.450 nonbonded pdb=" OE1 GLU A 643 " pdb=" H GLU A 643 " model vdw 1.788 2.450 nonbonded pdb=" OD1 ASN A 943 " pdb=" H ASP A 945 " model vdw 1.796 2.450 nonbonded pdb="HH11 ARG A1267 " pdb=" OD2 ASP A1285 " model vdw 1.796 2.450 nonbonded pdb=" H GLY A 833 " pdb=" O ASN A 875 " model vdw 1.810 2.450 ... (remaining 157489 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.050 Find NCS groups from input model: 0.090 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.003 0.100 5596 Z= 0.239 Angle : 1.323 71.250 7587 Z= 0.489 Chirality : 0.041 0.136 937 Planarity : 0.003 0.029 940 Dihedral : 13.128 89.815 2042 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.38 (0.32), residues: 720 helix: 2.18 (0.26), residues: 405 sheet: 1.20 (0.48), residues: 107 loop : 0.71 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1159 HIS 0.002 0.000 HIS A1016 PHE 0.006 0.001 PHE A1023 TYR 0.015 0.001 TYR A 716 ARG 0.001 0.000 ARG A 862 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2741 time to fit residues: 40.7696 Evaluate side-chains 89 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 0.0670 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN A1318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 5596 Z= 0.144 Angle : 0.901 30.471 7587 Z= 0.358 Chirality : 0.042 0.136 937 Planarity : 0.003 0.031 940 Dihedral : 3.475 16.325 762 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.66 % Allowed : 6.14 % Favored : 93.20 % 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: 2.67 (0.31), residues: 720 helix: 2.59 (0.25), residues: 414 sheet: 1.16 (0.48), residues: 107 loop : 0.40 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1159 HIS 0.002 0.001 HIS A1318 PHE 0.007 0.001 PHE A 951 TYR 0.006 0.001 TYR A 667 ARG 0.002 0.000 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 1181 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7646 (mptt) outliers start: 4 outliers final: 3 residues processed: 98 average time/residue: 0.2906 time to fit residues: 39.8372 Evaluate side-chains 96 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 0.0060 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5596 Z= 0.182 Angle : 0.901 30.016 7587 Z= 0.357 Chirality : 0.042 0.134 937 Planarity : 0.003 0.030 940 Dihedral : 3.521 17.294 762 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.50 % Allowed : 7.30 % Favored : 92.21 % 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: 2.73 (0.31), residues: 720 helix: 2.67 (0.25), residues: 419 sheet: 1.11 (0.48), residues: 105 loop : 0.33 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 936 HIS 0.003 0.001 HIS A1016 PHE 0.007 0.001 PHE A 951 TYR 0.004 0.001 TYR A 716 ARG 0.002 0.000 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 1202 ASP cc_start: 0.7756 (m-30) cc_final: 0.7544 (m-30) outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.3426 time to fit residues: 46.8161 Evaluate side-chains 99 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 1228 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 33 optimal weight: 0.0870 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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: 0.7734 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5596 Z= 0.141 Angle : 0.897 29.852 7587 Z= 0.351 Chirality : 0.042 0.131 937 Planarity : 0.003 0.035 940 Dihedral : 3.481 16.955 762 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.83 % Allowed : 8.79 % Favored : 90.38 % 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: 2.83 (0.31), residues: 720 helix: 2.86 (0.25), residues: 415 sheet: 1.06 (0.49), residues: 105 loop : 0.20 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 936 HIS 0.003 0.001 HIS A1253 PHE 0.006 0.001 PHE A 696 TYR 0.007 0.001 TYR A1075 ARG 0.001 0.000 ARG A1157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7573 (mm-30) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.3408 time to fit residues: 45.1674 Evaluate side-chains 98 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1228 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5596 Z= 0.166 Angle : 0.895 30.298 7587 Z= 0.352 Chirality : 0.042 0.138 937 Planarity : 0.003 0.034 940 Dihedral : 3.483 17.139 762 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.00 % Allowed : 8.62 % Favored : 90.38 % 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: 2.74 (0.31), residues: 720 helix: 2.76 (0.25), residues: 421 sheet: 0.93 (0.48), residues: 105 loop : 0.21 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 936 HIS 0.003 0.001 HIS A1016 PHE 0.006 0.001 PHE A 951 TYR 0.007 0.001 TYR A1075 ARG 0.001 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7436 (mm-30) outliers start: 6 outliers final: 4 residues processed: 103 average time/residue: 0.3215 time to fit residues: 45.3741 Evaluate side-chains 106 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1228 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.7809 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5596 Z= 0.221 Angle : 0.905 31.264 7587 Z= 0.360 Chirality : 0.042 0.134 937 Planarity : 0.003 0.034 940 Dihedral : 3.536 17.511 762 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.00 % Allowed : 9.95 % Favored : 89.05 % 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: 2.65 (0.32), residues: 720 helix: 2.70 (0.25), residues: 421 sheet: 0.77 (0.47), residues: 111 loop : 0.20 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 936 HIS 0.003 0.001 HIS A1016 PHE 0.008 0.001 PHE A 657 TYR 0.006 0.001 TYR A1075 ARG 0.002 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7433 (mm-30) REVERT: A 1264 ASP cc_start: 0.7402 (m-30) cc_final: 0.7174 (t0) outliers start: 6 outliers final: 5 residues processed: 105 average time/residue: 0.3521 time to fit residues: 50.2176 Evaluate side-chains 107 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1228 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 40.0000 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7836 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5596 Z= 0.224 Angle : 0.906 31.660 7587 Z= 0.362 Chirality : 0.042 0.136 937 Planarity : 0.003 0.033 940 Dihedral : 3.619 17.780 762 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.83 % Allowed : 9.95 % Favored : 89.22 % 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: 2.51 (0.32), residues: 720 helix: 2.60 (0.25), residues: 421 sheet: 0.68 (0.47), residues: 111 loop : 0.16 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 936 HIS 0.004 0.001 HIS A1253 PHE 0.010 0.001 PHE A 657 TYR 0.007 0.001 TYR A1075 ARG 0.002 0.000 ARG A1326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 1264 ASP cc_start: 0.7448 (m-30) cc_final: 0.6677 (t0) outliers start: 5 outliers final: 5 residues processed: 102 average time/residue: 0.3727 time to fit residues: 52.5207 Evaluate side-chains 104 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1228 ASP Chi-restraints excluded: chain A residue 1355 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5596 Z= 0.160 Angle : 0.900 30.545 7587 Z= 0.354 Chirality : 0.042 0.134 937 Planarity : 0.003 0.034 940 Dihedral : 3.542 17.567 762 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.66 % Allowed : 11.28 % Favored : 88.06 % 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: 2.62 (0.32), residues: 720 helix: 2.71 (0.25), residues: 421 sheet: 0.63 (0.46), residues: 113 loop : 0.18 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 936 HIS 0.002 0.001 HIS A1016 PHE 0.007 0.001 PHE A 696 TYR 0.004 0.001 TYR A1337 ARG 0.001 0.000 ARG A1326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 1264 ASP cc_start: 0.7441 (m-30) cc_final: 0.6663 (t0) outliers start: 4 outliers final: 4 residues processed: 104 average time/residue: 0.4159 time to fit residues: 58.1332 Evaluate side-chains 104 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1228 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5596 Z= 0.191 Angle : 0.900 31.256 7587 Z= 0.356 Chirality : 0.042 0.134 937 Planarity : 0.003 0.033 940 Dihedral : 3.569 17.726 762 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.66 % Allowed : 10.95 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.59 (0.32), residues: 720 helix: 2.71 (0.25), residues: 421 sheet: 0.61 (0.46), residues: 113 loop : 0.13 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 936 HIS 0.003 0.001 HIS A1016 PHE 0.008 0.001 PHE A 657 TYR 0.005 0.001 TYR A1337 ARG 0.002 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 855 THR cc_start: 0.8878 (m) cc_final: 0.8645 (p) REVERT: A 886 HIS cc_start: 0.7925 (m-70) cc_final: 0.7710 (m-70) REVERT: A 1228 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8285 (t70) REVERT: A 1264 ASP cc_start: 0.7442 (m-30) cc_final: 0.6701 (t0) outliers start: 4 outliers final: 3 residues processed: 101 average time/residue: 0.3578 time to fit residues: 49.5754 Evaluate side-chains 104 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1228 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5596 Z= 0.169 Angle : 0.896 30.652 7587 Z= 0.353 Chirality : 0.042 0.134 937 Planarity : 0.003 0.034 940 Dihedral : 3.532 17.484 762 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.66 % Allowed : 11.11 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.68 (0.32), residues: 720 helix: 2.77 (0.25), residues: 421 sheet: 0.67 (0.46), residues: 112 loop : 0.15 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 936 HIS 0.002 0.001 HIS A1016 PHE 0.008 0.001 PHE A 696 TYR 0.004 0.001 TYR A 712 ARG 0.001 0.000 ARG A1326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 1026 is missing expected H atoms. Skipping. Residue LEU 1042 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 855 THR cc_start: 0.8918 (m) cc_final: 0.8613 (p) REVERT: A 886 HIS cc_start: 0.7923 (m-70) cc_final: 0.7714 (m-70) REVERT: A 1228 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8274 (t70) REVERT: A 1264 ASP cc_start: 0.7443 (m-30) cc_final: 0.6701 (t0) outliers start: 4 outliers final: 3 residues processed: 103 average time/residue: 0.3353 time to fit residues: 47.1705 Evaluate side-chains 104 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1228 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.180813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.126749 restraints weight = 18398.597| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.52 r_work: 0.3124 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5596 Z= 0.133 Angle : 0.889 30.026 7587 Z= 0.346 Chirality : 0.042 0.132 937 Planarity : 0.003 0.034 940 Dihedral : 3.450 17.264 762 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.66 % Allowed : 11.11 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.78 (0.32), residues: 720 helix: 2.91 (0.25), residues: 421 sheet: 0.59 (0.45), residues: 123 loop : 0.12 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 936 HIS 0.002 0.000 HIS A1016 PHE 0.008 0.001 PHE A 696 TYR 0.004 0.001 TYR A 712 ARG 0.001 0.000 ARG A1267 =============================================================================== Job complete usr+sys time: 3092.64 seconds wall clock time: 54 minutes 33.53 seconds (3273.53 seconds total)