Starting phenix.real_space_refine on Sun Nov 17 00:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfh_40441/11_2024/8sfh_40441.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfh_40441/11_2024/8sfh_40441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfh_40441/11_2024/8sfh_40441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfh_40441/11_2024/8sfh_40441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfh_40441/11_2024/8sfh_40441.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfh_40441/11_2024/8sfh_40441.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 26 5.16 5 C 7638 2.51 5 N 2120 2.21 5 O 2533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12407 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10527 Classifications: {'peptide': 1286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1236} Chain breaks: 4 Chain: "B" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 568 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna2p': 6, 'rna3p': 20} Chain: "C" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 660 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 7.98, per 1000 atoms: 0.64 Number of scatterers: 12407 At special positions: 0 Unit cell: (96.628, 109.123, 146.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 90 15.00 O 2533 8.00 N 2120 7.00 C 7638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 56.1% alpha, 11.4% beta 34 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 3.856A pdb=" N GLN A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.667A pdb=" N ASN A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 134 through 140 removed outlier: 4.233A pdb=" N PHE A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.841A pdb=" N PHE A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.512A pdb=" N TYR A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 169 through 181 removed outlier: 4.303A pdb=" N ASN A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.163A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.802A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 289 through 298 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.647A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 420 through 428 removed outlier: 3.545A pdb=" N GLY A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.592A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 483 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.943A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 609 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.732A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.668A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 694 through 698 removed outlier: 4.243A pdb=" N SER A 697 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.584A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.670A pdb=" N ILE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.595A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 819 through 831 removed outlier: 4.033A pdb=" N GLN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 825 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 849 removed outlier: 3.619A pdb=" N VAL A 849 " --> pdb=" O LEU A 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 846 through 849' Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 954 Processing helix chain 'A' and resid 957 through 987 removed outlier: 3.656A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 4.157A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.685A pdb=" N PHE A1101 " --> pdb=" O PHE A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 4.619A pdb=" N LYS A1202 " --> pdb=" O ASN A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1284 removed outlier: 3.811A pdb=" N ASN A1265 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A1267 " --> pdb=" O ASP A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 removed outlier: 4.789A pdb=" N GLN A1303 " --> pdb=" O LEU A1299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.771A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.771A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.582A pdb=" N ILE A 418 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 807 Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.599A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 934 through 935 Processing sheet with id=AA8, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 4.009A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AB1, first strand: chain 'A' and resid 1159 through 1165 removed outlier: 5.181A pdb=" N ARG A1172 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU A1165 " --> pdb=" O THR A1170 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR A1170 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 4.509A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3000 1.33 - 1.46: 3398 1.46 - 1.58: 6247 1.58 - 1.70: 178 1.70 - 1.83: 44 Bond restraints: 12867 Sorted by residual: bond pdb=" C1' DT D 16 " pdb=" N1 DT D 16 " ideal model delta sigma weight residual 1.490 1.559 -0.069 3.00e-02 1.11e+03 5.36e+00 bond pdb=" CB THR A 16 " pdb=" CG2 THR A 16 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.02e+00 bond pdb=" CA HIS A 415 " pdb=" C HIS A 415 " ideal model delta sigma weight residual 1.522 1.552 -0.030 1.52e-02 4.33e+03 3.90e+00 bond pdb=" CA ARG A 794 " pdb=" CB ARG A 794 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.32e-02 5.74e+03 3.76e+00 bond pdb=" CG1 ILE A 979 " pdb=" CD1 ILE A 979 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.56e+00 ... (remaining 12862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 17482 3.35 - 6.70: 232 6.70 - 10.05: 43 10.05 - 13.40: 14 13.40 - 16.75: 5 Bond angle restraints: 17776 Sorted by residual: angle pdb=" CB MET A 732 " pdb=" CG MET A 732 " pdb=" SD MET A 732 " ideal model delta sigma weight residual 112.70 129.11 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CA LEU A 310 " pdb=" CB LEU A 310 " pdb=" CG LEU A 310 " ideal model delta sigma weight residual 116.30 133.05 -16.75 3.50e+00 8.16e-02 2.29e+01 angle pdb=" CA GLN A 937 " pdb=" CB GLN A 937 " pdb=" CG GLN A 937 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" O3' DT D 13 " pdb=" P DA D 14 " pdb=" OP1 DA D 14 " ideal model delta sigma weight residual 108.00 121.66 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C HIS A 415 " pdb=" CA HIS A 415 " pdb=" CB HIS A 415 " ideal model delta sigma weight residual 111.35 118.75 -7.40 1.72e+00 3.38e-01 1.85e+01 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 6984 29.39 - 58.78: 581 58.78 - 88.18: 63 88.18 - 117.57: 2 117.57 - 146.96: 2 Dihedral angle restraints: 7632 sinusoidal: 3835 harmonic: 3797 Sorted by residual: dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 53.04 146.96 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 54.63 145.37 1 1.50e+01 4.44e-03 7.78e+01 dihedral pdb=" CA PRO A 599 " pdb=" C PRO A 599 " pdb=" N ASP A 600 " pdb=" CA ASP A 600 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1768 0.092 - 0.185: 174 0.185 - 0.277: 16 0.277 - 0.369: 7 0.369 - 0.462: 7 Chirality restraints: 1972 Sorted by residual: chirality pdb=" P DC C 26 " pdb=" OP1 DC C 26 " pdb=" OP2 DC C 26 " pdb=" O5' DC C 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" P DA D 14 " pdb=" OP1 DA D 14 " pdb=" OP2 DA D 14 " pdb=" O5' DA D 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" P DC C 24 " pdb=" OP1 DC C 24 " pdb=" OP2 DC C 24 " pdb=" O5' DC C 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 1969 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1255 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A1256 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A1256 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A1256 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1207 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ASP A1207 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP A1207 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP A1208 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 440 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C SER A 440 " -0.050 2.00e-02 2.50e+03 pdb=" O SER A 440 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 441 " 0.017 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2746 2.79 - 3.32: 11640 3.32 - 3.84: 21454 3.84 - 4.37: 25161 4.37 - 4.90: 40855 Nonbonded interactions: 101856 Sorted by model distance: nonbonded pdb=" OD2 ASP A 326 " pdb=" OG1 THR A 457 " model vdw 2.261 3.040 nonbonded pdb=" O ARG A 862 " pdb=" OG1 THR A 865 " model vdw 2.275 3.040 nonbonded pdb=" NH2 ARG A 863 " pdb=" OP2 C B 6 " model vdw 2.297 3.120 nonbonded pdb=" OG1 THR A 151 " pdb=" OD1 ASN A 156 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 922 " pdb=" NE2 GLN A1275 " model vdw 2.317 3.120 ... (remaining 101851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.110 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12867 Z= 0.355 Angle : 1.073 16.745 17776 Z= 0.545 Chirality : 0.064 0.462 1972 Planarity : 0.007 0.116 1959 Dihedral : 19.219 146.960 5172 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.52 % Allowed : 13.19 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1276 helix: 0.43 (0.20), residues: 629 sheet: 0.24 (0.41), residues: 144 loop : 0.36 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 382 HIS 0.008 0.002 HIS A 368 PHE 0.027 0.003 PHE A1253 TYR 0.037 0.003 TYR A 83 ARG 0.020 0.001 ARG A1194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 1.270 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.2685 time to fit residues: 22.8863 Evaluate side-chains 39 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 206 HIS A 552 ASN A 800 HIS ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS A1167 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12867 Z= 0.337 Angle : 0.645 9.998 17776 Z= 0.345 Chirality : 0.042 0.147 1972 Planarity : 0.004 0.076 1959 Dihedral : 20.064 151.472 2511 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.74 % Allowed : 11.37 % Favored : 86.89 % 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: 1.29 (0.24), residues: 1276 helix: 1.31 (0.21), residues: 645 sheet: -0.08 (0.40), residues: 141 loop : 0.75 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 382 HIS 0.007 0.001 HIS A 415 PHE 0.017 0.002 PHE A1249 TYR 0.016 0.002 TYR A 61 ARG 0.007 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 1.387 Fit side-chains outliers start: 20 outliers final: 5 residues processed: 53 average time/residue: 0.2338 time to fit residues: 19.9596 Evaluate side-chains 35 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1290 GLN A1303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12867 Z= 0.286 Angle : 0.589 9.398 17776 Z= 0.315 Chirality : 0.040 0.138 1972 Planarity : 0.004 0.059 1959 Dihedral : 20.073 153.844 2509 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.48 % Allowed : 11.98 % Favored : 86.55 % 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: 1.72 (0.25), residues: 1276 helix: 1.77 (0.21), residues: 647 sheet: -0.13 (0.39), residues: 143 loop : 0.89 (0.32), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 382 HIS 0.007 0.001 HIS A 415 PHE 0.014 0.001 PHE A 198 TYR 0.017 0.001 TYR A 595 ARG 0.004 0.000 ARG A1194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 1.473 Fit side-chains REVERT: A 795 MET cc_start: 0.7940 (tpp) cc_final: 0.7591 (mmm) REVERT: A 806 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.6849 (ttm) outliers start: 17 outliers final: 6 residues processed: 48 average time/residue: 0.2535 time to fit residues: 19.6869 Evaluate side-chains 38 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS A1303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12867 Z= 0.308 Angle : 0.594 11.468 17776 Z= 0.316 Chirality : 0.040 0.133 1972 Planarity : 0.003 0.048 1959 Dihedral : 20.099 154.917 2509 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.48 % Allowed : 12.50 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1276 helix: 1.99 (0.21), residues: 643 sheet: 0.03 (0.41), residues: 143 loop : 0.90 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 382 HIS 0.006 0.001 HIS A1269 PHE 0.014 0.001 PHE A 138 TYR 0.019 0.002 TYR A 61 ARG 0.004 0.000 ARG A1194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 47 average time/residue: 0.2357 time to fit residues: 18.1853 Evaluate side-chains 39 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 0.0980 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12867 Z= 0.298 Angle : 0.581 10.897 17776 Z= 0.309 Chirality : 0.040 0.164 1972 Planarity : 0.003 0.044 1959 Dihedral : 20.136 154.194 2509 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.22 % Allowed : 13.45 % Favored : 85.33 % 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: 2.00 (0.25), residues: 1276 helix: 2.04 (0.21), residues: 649 sheet: 0.11 (0.41), residues: 142 loop : 0.90 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 382 HIS 0.006 0.001 HIS A1269 PHE 0.014 0.001 PHE A 138 TYR 0.017 0.001 TYR A 61 ARG 0.002 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 1.263 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 44 average time/residue: 0.2168 time to fit residues: 15.7571 Evaluate side-chains 38 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 40.0000 chunk 69 optimal weight: 0.0270 chunk 126 optimal weight: 0.8980 overall best weight: 2.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12867 Z= 0.234 Angle : 0.547 10.172 17776 Z= 0.290 Chirality : 0.039 0.143 1972 Planarity : 0.003 0.040 1959 Dihedral : 20.085 152.521 2509 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.13 % Allowed : 13.63 % Favored : 85.24 % 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: 2.21 (0.25), residues: 1276 helix: 2.32 (0.21), residues: 636 sheet: 0.24 (0.41), residues: 138 loop : 0.84 (0.31), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 382 HIS 0.005 0.001 HIS A1269 PHE 0.011 0.001 PHE A 198 TYR 0.015 0.001 TYR A 83 ARG 0.002 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 1.449 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 42 average time/residue: 0.2290 time to fit residues: 16.1844 Evaluate side-chains 38 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12867 Z= 0.254 Angle : 0.558 9.871 17776 Z= 0.295 Chirality : 0.039 0.187 1972 Planarity : 0.003 0.040 1959 Dihedral : 20.125 152.428 2509 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 13.72 % Favored : 85.07 % 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: 2.22 (0.25), residues: 1276 helix: 2.30 (0.21), residues: 644 sheet: 0.28 (0.41), residues: 138 loop : 0.85 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 382 HIS 0.005 0.001 HIS A1269 PHE 0.012 0.001 PHE A 198 TYR 0.016 0.001 TYR A 173 ARG 0.005 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 1.316 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 46 average time/residue: 0.2235 time to fit residues: 16.9856 Evaluate side-chains 38 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1051 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 12867 Z= 0.412 Angle : 0.654 10.763 17776 Z= 0.343 Chirality : 0.042 0.235 1972 Planarity : 0.004 0.043 1959 Dihedral : 20.348 155.211 2509 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.22 % Allowed : 14.84 % Favored : 83.94 % 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: 2.02 (0.25), residues: 1276 helix: 2.12 (0.21), residues: 648 sheet: 0.11 (0.41), residues: 143 loop : 0.82 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 382 HIS 0.007 0.001 HIS A1269 PHE 0.016 0.002 PHE A 198 TYR 0.021 0.002 TYR A 61 ARG 0.004 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 1.346 Fit side-chains REVERT: A 168 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: A 795 MET cc_start: 0.8067 (tpp) cc_final: 0.7666 (mmm) outliers start: 14 outliers final: 10 residues processed: 41 average time/residue: 0.2425 time to fit residues: 16.1680 Evaluate side-chains 40 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.1980 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 646 ASN A 977 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 12867 Z= 0.146 Angle : 0.562 11.350 17776 Z= 0.291 Chirality : 0.038 0.186 1972 Planarity : 0.003 0.037 1959 Dihedral : 20.039 149.805 2509 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.78 % Allowed : 15.54 % Favored : 83.68 % 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: 2.26 (0.25), residues: 1276 helix: 2.38 (0.21), residues: 638 sheet: 0.32 (0.41), residues: 141 loop : 0.84 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 977 PHE 0.009 0.001 PHE A 871 TYR 0.015 0.001 TYR A 83 ARG 0.006 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 795 MET cc_start: 0.7986 (tpp) cc_final: 0.7589 (mmm) outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.2294 time to fit residues: 16.9153 Evaluate side-chains 37 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12867 Z= 0.253 Angle : 0.590 12.746 17776 Z= 0.305 Chirality : 0.039 0.185 1972 Planarity : 0.003 0.037 1959 Dihedral : 20.089 150.522 2509 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.61 % Allowed : 16.06 % Favored : 83.33 % 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: 2.29 (0.25), residues: 1276 helix: 2.39 (0.21), residues: 643 sheet: 0.38 (0.41), residues: 141 loop : 0.83 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.005 0.001 HIS A1269 PHE 0.012 0.001 PHE A 198 TYR 0.026 0.001 TYR A 173 ARG 0.005 0.000 ARG A 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 795 MET cc_start: 0.8020 (tpp) cc_final: 0.7601 (mmm) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.1762 time to fit residues: 11.2113 Evaluate side-chains 39 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.042919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.029966 restraints weight = 74445.243| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 4.08 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12867 Z= 0.240 Angle : 0.588 13.070 17776 Z= 0.304 Chirality : 0.039 0.186 1972 Planarity : 0.003 0.036 1959 Dihedral : 20.138 151.151 2509 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.87 % Allowed : 15.80 % Favored : 83.33 % 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: 2.33 (0.25), residues: 1276 helix: 2.45 (0.21), residues: 637 sheet: 0.40 (0.41), residues: 141 loop : 0.84 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS A1269 PHE 0.011 0.001 PHE A 198 TYR 0.019 0.001 TYR A 173 ARG 0.004 0.000 ARG A 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.14 seconds wall clock time: 48 minutes 24.61 seconds (2904.61 seconds total)