Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 03:05:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/04_2023/7si7_25139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/04_2023/7si7_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_25139/04_2023/7si7_25139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/04_2023/7si7_25139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/04_2023/7si7_25139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7si7_25139/04_2023/7si7_25139_updated.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 820": "OE1" <-> "OE2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A GLU 1248": "OE1" <-> "OE2" Residue "A ASP 1285": "OD1" <-> "OD2" Residue "A GLU 1299": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11287 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 11287 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 728, 'undetermined': 2} Link IDs: {'PTRANS': 28, 'TRANS': 699, None: 2} Not linked: pdbres="ASP A1413 " pdbres=" MG A1501 " Not linked: pdbres=" MG A1501 " pdbres="ALF A1502 " 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 Time building chain proxies: 5.22, per 1000 atoms: 0.46 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 - 3.50 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: 9.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 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... running ksdssp... Secondary structure from input PDB file: 29 helices and 5 sheets defined 52.9% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 641 through 670 Proline residue: A 660 - end of helix Processing helix chain 'A' and resid 679 through 682 No H-bonds generated for 'chain 'A' and resid 679 through 682' Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 726 through 751 Processing helix chain 'A' and resid 761 through 782 Proline residue: A 765 - end of helix Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 892 through 906 Processing helix chain 'A' and resid 913 through 942 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 945 through 950 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 960 through 979 Processing helix chain 'A' and resid 983 through 986 Processing helix chain 'A' and resid 988 through 1001 Processing helix chain 'A' and resid 1010 through 1017 removed outlier: 4.756A pdb=" N HIS A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 Processing helix chain 'A' and resid 1067 through 1079 Processing helix chain 'A' and resid 1106 through 1111 Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'A' and resid 1169 through 1180 Processing helix chain 'A' and resid 1208 through 1217 Processing helix chain 'A' and resid 1230 through 1240 Processing helix chain 'A' and resid 1251 through 1263 Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1310 through 1345 removed outlier: 3.549A pdb=" N SER A1316 " --> pdb=" O VAL A1313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1319 " --> pdb=" O SER A1316 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A1336 " --> pdb=" O PHE A1333 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR A1337 " --> pdb=" O ALA A1334 " (cutoff:3.500A) Proline residue: A1343 - end of helix Processing helix chain 'A' and resid 1358 through 1381 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) removed outlier: 4.359A pdb=" N LYS A1380 " --> pdb=" O SER A1376 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N CYS A1381 " --> pdb=" O LEU A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1393 Processing sheet with id= A, first strand: chain 'A' and resid 799 through 803 Processing sheet with id= B, first strand: chain 'A' and resid 827 through 830 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= C, first strand: chain 'A' and resid 861 through 863 Processing sheet with id= D, first strand: chain 'A' and resid 1004 through 1006 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: 6.076A pdb=" N ASP A1221 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE A1023 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A1223 " --> pdb=" O PHE A1023 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A1244 " --> pdb=" O LEU A1224 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER A1407 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A1247 " --> pdb=" O SER A1407 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A1409 " --> pdb=" O ALA A1247 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 6.737A pdb=" N VAL A1188 " --> pdb=" O CYS A1195 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N MET A1197 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A1186 " --> pdb=" O MET A1197 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA A1199 " --> pdb=" O THR A1184 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A1184 " --> pdb=" O ALA A1199 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 777 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: 4.21 Time building geometry restraints manager: 9.72 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: 89.92 - 107.93: 1556 107.93 - 125.94: 19078 125.94 - 143.95: 94 143.95 - 161.96: 0 161.96 - 179.97: 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: 4136 17.96 - 35.93: 298 35.93 - 53.89: 31 53.89 - 71.85: 5 71.85 - 89.82: 5 Dihedral angle restraints: 4475 sinusoidal: 2127 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 4472 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: 1.72 - 2.29: 2162 2.29 - 2.87: 26867 2.87 - 3.45: 29195 3.45 - 4.02: 39523 4.02 - 4.60: 60011 Nonbonded interactions: 157758 Sorted by model distance: nonbonded pdb=" O ASP A1312 " pdb=" H SER A1316 " model vdw 1.715 1.850 nonbonded pdb=" O ALA A1367 " pdb=" HG SER A1371 " model vdw 1.740 1.850 nonbonded pdb=" O VAL A1057 " pdb=" H GLU A1061 " model vdw 1.751 1.850 nonbonded pdb=" OE1 GLU A 643 " pdb=" H GLU A 643 " model vdw 1.788 1.850 nonbonded pdb=" O VAL A1332 " pdb=" H ILE A1336 " model vdw 1.794 1.850 ... (remaining 157753 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: 0.110 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: 0.170 Extract box with map and model: 1.590 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.510 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.780 ------------------------------------------------------------------------------- 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= 0.208 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 % 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 *********************** 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 : 0.908 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: 0.2819 time to fit residues: 41.8442 Evaluate side-chains 89 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 5596 Z= 0.183 Angle : 0.895 31.283 7587 Z= 0.352 Chirality : 0.042 0.149 937 Planarity : 0.003 0.028 940 Dihedral : 3.430 14.039 762 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.00 % 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: 2.61 (0.31), residues: 720 helix: 2.48 (0.26), residues: 402 sheet: 1.24 (0.48), residues: 107 loop : 0.59 (0.44), residues: 211 *********************** 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 99 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 95 average time/residue: 0.3298 time to fit residues: 42.6280 Evaluate side-chains 95 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1429 time to fit residues: 1.8163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 30.0000 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.7740 moved from start: 0.1093 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= 0.133 Angle : 0.885 29.728 7587 Z= 0.343 Chirality : 0.041 0.131 937 Planarity : 0.003 0.029 940 Dihedral : 3.347 14.617 762 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.70 (0.32), residues: 720 helix: 2.56 (0.26), residues: 407 sheet: 1.30 (0.49), residues: 107 loop : 0.54 (0.44), residues: 206 *********************** 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 98 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 96 average time/residue: 0.3273 time to fit residues: 43.2633 Evaluate side-chains 95 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1574 time to fit residues: 1.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.1980 chunk 49 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 5596 Z= 0.151 Angle : 0.890 30.487 7587 Z= 0.346 Chirality : 0.041 0.131 937 Planarity : 0.003 0.035 940 Dihedral : 3.340 14.327 762 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.32), residues: 720 helix: 2.70 (0.26), residues: 402 sheet: 1.30 (0.49), residues: 107 loop : 0.48 (0.44), residues: 211 *********************** 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 103 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 0.3610 time to fit residues: 49.6581 Evaluate side-chains 99 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1674 time to fit residues: 1.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 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: 0.7824 moved from start: 0.1692 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= 0.220 Angle : 0.902 31.351 7587 Z= 0.358 Chirality : 0.042 0.136 937 Planarity : 0.003 0.035 940 Dihedral : 3.479 13.881 762 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.43 (0.32), residues: 720 helix: 2.34 (0.26), residues: 408 sheet: 1.27 (0.49), residues: 107 loop : 0.38 (0.44), residues: 205 *********************** 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 101 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 99 average time/residue: 0.3444 time to fit residues: 46.2079 Evaluate side-chains 97 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1236 time to fit residues: 1.3317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5596 Z= 0.245 Angle : 0.912 31.638 7587 Z= 0.365 Chirality : 0.042 0.143 937 Planarity : 0.003 0.036 940 Dihedral : 3.591 13.888 762 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.31), residues: 720 helix: 2.17 (0.26), residues: 406 sheet: 1.19 (0.48), residues: 107 loop : 0.26 (0.43), residues: 207 *********************** 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 104 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.3433 time to fit residues: 47.2742 Evaluate side-chains 101 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1535 time to fit residues: 1.5502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 5596 Z= 0.286 Angle : 0.917 32.008 7587 Z= 0.371 Chirality : 0.043 0.151 937 Planarity : 0.003 0.035 940 Dihedral : 3.735 15.040 762 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.00 % 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: 1.94 (0.31), residues: 720 helix: 1.94 (0.26), residues: 404 sheet: 0.99 (0.48), residues: 107 loop : 0.27 (0.44), residues: 209 *********************** 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: 6 poor density : 100 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 0.3573 time to fit residues: 49.2390 Evaluate side-chains 99 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1730 time to fit residues: 1.7729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 5596 Z= 0.248 Angle : 0.915 31.336 7587 Z= 0.366 Chirality : 0.042 0.169 937 Planarity : 0.003 0.035 940 Dihedral : 3.704 14.989 762 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.89 (0.31), residues: 720 helix: 1.92 (0.26), residues: 405 sheet: 0.89 (0.48), residues: 107 loop : 0.25 (0.44), residues: 208 *********************** 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 100 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.3523 time to fit residues: 47.1304 Evaluate side-chains 98 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2452 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= 0.216 Angle : 0.905 31.000 7587 Z= 0.360 Chirality : 0.042 0.181 937 Planarity : 0.003 0.035 940 Dihedral : 3.653 15.143 762 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.66 % 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: 1.91 (0.32), residues: 720 helix: 1.95 (0.26), residues: 406 sheet: 0.83 (0.48), residues: 107 loop : 0.23 (0.45), residues: 207 *********************** 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 101 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.3568 time to fit residues: 46.8652 Evaluate side-chains 100 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1723 time to fit residues: 2.0734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 40.0000 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5596 Z= 0.225 Angle : 0.910 31.003 7587 Z= 0.363 Chirality : 0.042 0.199 937 Planarity : 0.003 0.033 940 Dihedral : 3.640 14.864 762 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.90 (0.32), residues: 720 helix: 1.96 (0.26), residues: 405 sheet: 0.69 (0.49), residues: 101 loop : 0.32 (0.44), residues: 214 ********************** 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 100 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.3622 time to fit residues: 48.6101 Evaluate side-chains 98 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 58 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.178024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.123743 restraints weight = 18489.773| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.48 r_work: 0.3089 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 5596 Z= 0.142 Angle : 0.899 29.900 7587 Z= 0.351 Chirality : 0.042 0.185 937 Planarity : 0.003 0.035 940 Dihedral : 3.473 14.428 762 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.32), residues: 720 helix: 2.18 (0.26), residues: 410 sheet: 0.70 (0.49), residues: 101 loop : 0.25 (0.44), residues: 209 =============================================================================== Job complete usr+sys time: 2936.04 seconds wall clock time: 52 minutes 40.68 seconds (3160.68 seconds total)