Starting phenix.real_space_refine (version: dev) on Sun Feb 19 04:50:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmq_30767/02_2023/7dmq_30767.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmq_30767/02_2023/7dmq_30767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmq_30767/02_2023/7dmq_30767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmq_30767/02_2023/7dmq_30767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmq_30767/02_2023/7dmq_30767.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmq_30767/02_2023/7dmq_30767.pdb" } resolution = 3.06 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "A TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1194": "NH1" <-> "NH2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1312": "NH1" <-> "NH2" Residue "A PHE 1340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1351": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9444 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 7575 Classifications: {'peptide': 937} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 10, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 175 Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1125 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 5, 'rna3p': 47} Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 744 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 2, 'rna3p': 32} Time building chain proxies: 6.05, per 1000 atoms: 0.64 Number of scatterers: 9444 At special positions: 0 Unit cell: (102.495, 110.246, 126.611, 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 14 16.00 P 88 15.00 O 2051 8.00 N 1586 7.00 C 5705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 3 sheets defined 54.3% alpha, 1.1% beta 26 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 342 through 346 removed outlier: 4.139A pdb=" N ILE A 345 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.763A pdb=" N PHE A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 5.339A pdb=" N GLU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 421 through 448 Processing helix chain 'A' and resid 471 through 493 removed outlier: 3.650A pdb=" N LEU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 512 through 524 removed outlier: 3.656A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.845A pdb=" N ILE A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.997A pdb=" N ASN A 580 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 602 removed outlier: 3.766A pdb=" N ILE A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 596 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 628 removed outlier: 4.383A pdb=" N ILE A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 672 through 685 removed outlier: 3.701A pdb=" N VAL A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) Proline residue: A 678 - end of helix Processing helix chain 'A' and resid 699 through 718 removed outlier: 4.363A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 718 " --> pdb=" O TYR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 741 removed outlier: 4.262A pdb=" N GLU A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 789 removed outlier: 3.894A pdb=" N LYS A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 788 " --> pdb=" O TYR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 834 through 845 removed outlier: 3.578A pdb=" N ILE A 842 " --> pdb=" O TYR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 867 removed outlier: 3.592A pdb=" N ASN A 857 " --> pdb=" O ASN A 853 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 872 through 882 removed outlier: 3.763A pdb=" N ASP A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 877 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 879 " --> pdb=" O ILE A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 911 removed outlier: 3.964A pdb=" N GLN A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1033 Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1071 through 1077 removed outlier: 3.501A pdb=" N ILE A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A1077 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1093 through 1097 removed outlier: 3.537A pdb=" N GLY A1096 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1149 through 1170 removed outlier: 3.730A pdb=" N ASP A1155 " --> pdb=" O SER A1151 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A1167 " --> pdb=" O LYS A1163 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1209 removed outlier: 4.023A pdb=" N GLN A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A1196 " --> pdb=" O MET A1192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A1200 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A1203 " --> pdb=" O MET A1199 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A1209 " --> pdb=" O GLY A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1260 removed outlier: 3.620A pdb=" N TYR A1249 " --> pdb=" O ASP A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 Processing helix chain 'A' and resid 1284 through 1289 removed outlier: 3.627A pdb=" N ARG A1288 " --> pdb=" O PHE A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1305 removed outlier: 3.860A pdb=" N ASP A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A1302 " --> pdb=" O GLU A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1322 removed outlier: 3.718A pdb=" N PHE A1322 " --> pdb=" O TYR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1327 removed outlier: 3.626A pdb=" N LYS A1326 " --> pdb=" O GLU A1323 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A1327 " --> pdb=" O VAL A1324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1323 through 1327' Processing helix chain 'A' and resid 1332 through 1337 Processing helix chain 'A' and resid 1367 through 1381 removed outlier: 3.574A pdb=" N THR A1380 " --> pdb=" O ILE A1376 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A1381 " --> pdb=" O GLU A1377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA2, first strand: chain 'A' and resid 1216 through 1217 Processing sheet with id=AA3, first strand: chain 'A' and resid 1329 through 1331 294 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 4.52 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: 2098 1.33 - 1.45: 2556 1.45 - 1.58: 4930 1.58 - 1.70: 174 1.70 - 1.82: 24 Bond restraints: 9782 Sorted by residual: bond pdb=" CB ASP A 381 " pdb=" CG ASP A 381 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" CB VAL A1287 " pdb=" CG1 VAL A1287 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" N ASP A 494 " pdb=" CA ASP A 494 " ideal model delta sigma weight residual 1.460 1.481 -0.021 1.42e-02 4.96e+03 2.21e+00 bond pdb=" CA ASP A 381 " pdb=" CB ASP A 381 " ideal model delta sigma weight residual 1.535 1.555 -0.020 1.37e-02 5.33e+03 2.19e+00 bond pdb=" C LEU A 677 " pdb=" N PRO A 678 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.16e+00 ... (remaining 9777 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.79: 503 105.79 - 112.86: 5058 112.86 - 119.92: 3844 119.92 - 126.98: 3951 126.98 - 134.04: 245 Bond angle restraints: 13601 Sorted by residual: angle pdb=" C ASN A 493 " pdb=" N ASP A 494 " pdb=" CA ASP A 494 " ideal model delta sigma weight residual 122.82 130.14 -7.32 1.42e+00 4.96e-01 2.66e+01 angle pdb=" C GLU A1265 " pdb=" N ASN A1266 " pdb=" CA ASN A1266 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C ILE A 380 " pdb=" N ASP A 381 " pdb=" CA ASP A 381 " ideal model delta sigma weight residual 125.02 133.25 -8.23 1.76e+00 3.23e-01 2.18e+01 angle pdb=" C ASN A 897 " pdb=" N LEU A 898 " pdb=" CA LEU A 898 " ideal model delta sigma weight residual 121.26 128.04 -6.78 1.59e+00 3.96e-01 1.82e+01 angle pdb=" C ASN A 899 " pdb=" N LEU A 900 " pdb=" CA LEU A 900 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 ... (remaining 13596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5665 35.81 - 71.62: 95 71.62 - 107.43: 10 107.43 - 143.24: 1 143.24 - 179.05: 3 Dihedral angle restraints: 5774 sinusoidal: 2963 harmonic: 2811 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 47.72 152.28 1 1.50e+01 4.44e-03 8.04e+01 dihedral pdb=" O4' U C 3 " pdb=" C1' U C 3 " pdb=" N1 U C 3 " pdb=" C2 U C 3 " ideal model delta sinusoidal sigma weight residual 200.00 49.29 150.71 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" O4' U B 54 " pdb=" C1' U B 54 " pdb=" N1 U B 54 " pdb=" C2 U B 54 " ideal model delta sinusoidal sigma weight residual -160.00 -22.03 -137.97 1 1.50e+01 4.44e-03 7.44e+01 ... (remaining 5771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1162 0.053 - 0.107: 362 0.107 - 0.160: 58 0.160 - 0.213: 12 0.213 - 0.267: 8 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CA ASP A 381 " pdb=" N ASP A 381 " pdb=" C ASP A 381 " pdb=" CB ASP A 381 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASP A 494 " pdb=" N ASP A 494 " pdb=" C ASP A 494 " pdb=" CB ASP A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN A1266 " pdb=" N ASN A1266 " pdb=" C ASN A1266 " pdb=" CB ASN A1266 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1599 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1053 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C LYS A1053 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A1053 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A1054 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 11 " 0.027 2.00e-02 2.50e+03 1.32e-02 3.92e+00 pdb=" N1 U C 11 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U C 11 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U C 11 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U C 11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U C 11 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U C 11 " 0.012 2.00e-02 2.50e+03 pdb=" C5 U C 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U C 11 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 825 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C THR A 825 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A 825 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 826 " 0.011 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1747 2.77 - 3.30: 8593 3.30 - 3.84: 15905 3.84 - 4.37: 18841 4.37 - 4.90: 29240 Nonbonded interactions: 74326 Sorted by model distance: nonbonded pdb=" OH TYR A1180 " pdb=" OD2 ASP A1328 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR A 613 " pdb=" OD2 ASP A 835 " model vdw 2.306 2.440 nonbonded pdb=" OD1 ASP A1301 " pdb=" OH TYR A1318 " model vdw 2.316 2.440 nonbonded pdb=" O ASN A 649 " pdb=" OG1 THR A 652 " model vdw 2.326 2.440 nonbonded pdb=" O2' A B 10 " pdb=" OP2 U B 12 " model vdw 2.329 2.440 ... (remaining 74321 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 88 5.49 5 S 14 5.16 5 C 5705 2.51 5 N 1586 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.890 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: 4.160 Check model and map are aligned: 0.150 Process input model: 30.630 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.005 0.056 9782 Z= 0.335 Angle : 0.958 9.732 13601 Z= 0.502 Chirality : 0.054 0.267 1602 Planarity : 0.005 0.045 1412 Dihedral : 13.950 179.054 3948 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -5.19 (0.20), residues: 929 helix: -3.21 (0.15), residues: 542 sheet: -2.33 (2.15), residues: 10 loop : -3.70 (0.25), residues: 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 213 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 216 average time/residue: 0.3345 time to fit residues: 91.7879 Evaluate side-chains 103 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0932 time to fit residues: 1.5330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 42 optimal weight: 0.1980 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 493 ASN A 563 ASN A 622 ASN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN A 710 ASN A 815 ASN A 849 ASN A1062 ASN A1066 ASN A1204 ASN A1305 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9782 Z= 0.155 Angle : 0.589 7.167 13601 Z= 0.310 Chirality : 0.040 0.195 1602 Planarity : 0.003 0.040 1412 Dihedral : 13.426 175.725 2064 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.71 (0.24), residues: 929 helix: -1.81 (0.20), residues: 540 sheet: -2.15 (2.12), residues: 10 loop : -3.42 (0.27), residues: 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.996 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 116 average time/residue: 0.2540 time to fit residues: 39.9823 Evaluate side-chains 97 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0857 time to fit residues: 1.8046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.0470 chunk 91 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9782 Z= 0.175 Angle : 0.567 6.610 13601 Z= 0.297 Chirality : 0.040 0.189 1602 Planarity : 0.003 0.040 1412 Dihedral : 13.147 174.617 2064 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.99 (0.25), residues: 929 helix: -1.16 (0.21), residues: 546 sheet: -2.20 (2.07), residues: 10 loop : -3.23 (0.27), residues: 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 124 average time/residue: 0.2801 time to fit residues: 45.7096 Evaluate side-chains 95 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1475 time to fit residues: 2.4349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9782 Z= 0.227 Angle : 0.597 7.775 13601 Z= 0.313 Chirality : 0.041 0.184 1602 Planarity : 0.003 0.041 1412 Dihedral : 13.095 172.268 2064 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.26), residues: 929 helix: -0.86 (0.22), residues: 548 sheet: -2.48 (1.93), residues: 10 loop : -3.09 (0.29), residues: 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 119 average time/residue: 0.2577 time to fit residues: 41.7475 Evaluate side-chains 103 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1056 time to fit residues: 2.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 9782 Z= 0.298 Angle : 0.650 9.040 13601 Z= 0.335 Chirality : 0.043 0.188 1602 Planarity : 0.004 0.055 1412 Dihedral : 13.107 172.545 2064 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.46 (0.27), residues: 929 helix: -0.78 (0.22), residues: 543 sheet: -2.33 (1.97), residues: 10 loop : -2.89 (0.30), residues: 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.061 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 115 average time/residue: 0.2804 time to fit residues: 43.3996 Evaluate side-chains 102 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0932 time to fit residues: 3.0990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0670 chunk 19 optimal weight: 0.0170 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 9782 Z= 0.145 Angle : 0.544 6.898 13601 Z= 0.281 Chirality : 0.039 0.191 1602 Planarity : 0.003 0.036 1412 Dihedral : 12.733 169.113 2064 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer Outliers : 0.99 % 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: -2.08 (0.27), residues: 929 helix: -0.38 (0.23), residues: 549 sheet: -2.31 (1.99), residues: 10 loop : -2.92 (0.29), residues: 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 110 average time/residue: 0.2765 time to fit residues: 41.1745 Evaluate side-chains 94 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0962 time to fit residues: 1.8185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.0000 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9782 Z= 0.257 Angle : 0.623 6.594 13601 Z= 0.322 Chirality : 0.043 0.209 1602 Planarity : 0.004 0.046 1412 Dihedral : 12.866 168.996 2064 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.13 (0.27), residues: 929 helix: -0.42 (0.22), residues: 544 sheet: -2.26 (1.98), residues: 10 loop : -2.93 (0.29), residues: 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.099 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 104 average time/residue: 0.2876 time to fit residues: 40.2111 Evaluate side-chains 97 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1002 time to fit residues: 2.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9782 Z= 0.172 Angle : 0.580 9.525 13601 Z= 0.299 Chirality : 0.040 0.228 1602 Planarity : 0.003 0.040 1412 Dihedral : 12.795 168.154 2064 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % 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: -1.97 (0.27), residues: 929 helix: -0.26 (0.23), residues: 544 sheet: -2.24 (2.00), residues: 10 loop : -2.91 (0.29), residues: 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 0.2834 time to fit residues: 39.1095 Evaluate side-chains 94 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0907 time to fit residues: 1.4378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 9782 Z= 0.282 Angle : 0.647 7.539 13601 Z= 0.335 Chirality : 0.044 0.210 1602 Planarity : 0.004 0.051 1412 Dihedral : 12.918 168.249 2064 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.15 (0.27), residues: 929 helix: -0.45 (0.22), residues: 545 sheet: -2.22 (1.97), residues: 10 loop : -2.93 (0.29), residues: 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.964 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.2854 time to fit residues: 40.0956 Evaluate side-chains 99 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0957 time to fit residues: 2.5018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9782 Z= 0.153 Angle : 0.563 7.193 13601 Z= 0.291 Chirality : 0.039 0.243 1602 Planarity : 0.003 0.041 1412 Dihedral : 12.584 164.298 2064 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer Outliers : 0.37 % 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: -1.78 (0.27), residues: 929 helix: -0.08 (0.23), residues: 542 sheet: -2.28 (1.99), residues: 10 loop : -2.84 (0.29), residues: 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 1.003 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 106 average time/residue: 0.2839 time to fit residues: 40.2919 Evaluate side-chains 97 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0988 time to fit residues: 1.5925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 82 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.190491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.153977 restraints weight = 11671.789| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.60 r_work: 0.3556 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9782 Z= 0.202 Angle : 0.598 7.719 13601 Z= 0.309 Chirality : 0.042 0.228 1602 Planarity : 0.004 0.067 1412 Dihedral : 12.608 162.727 2064 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer Outliers : 0.37 % 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: -1.79 (0.27), residues: 929 helix: -0.12 (0.23), residues: 544 sheet: -2.25 (1.98), residues: 10 loop : -2.82 (0.29), residues: 375 =============================================================================== Job complete usr+sys time: 1985.87 seconds wall clock time: 37 minutes 11.63 seconds (2231.63 seconds total)