Starting phenix.real_space_refine on Thu Jun 27 18:06:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6u_18963/06_2024/8r6u_18963.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6u_18963/06_2024/8r6u_18963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6u_18963/06_2024/8r6u_18963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6u_18963/06_2024/8r6u_18963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6u_18963/06_2024/8r6u_18963.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6u_18963/06_2024/8r6u_18963.pdb" } resolution = 2.98 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= 0.000 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 72 5.16 5 C 8346 2.51 5 N 2338 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1373": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12495 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1566, 12479 Classifications: {'peptide': 1566} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1566, 12479 Classifications: {'peptide': 1566} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1506} Chain breaks: 4 bond proxies already assigned to first conformer: 12726 Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 6, 'rna3p': 10} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.45, per 1000 atoms: 1.00 Number of scatterers: 13408 At special positions: 0 Unit cell: (101.15, 109.65, 127.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 41 15.00 Mg 1 11.99 O 2610 8.00 N 2338 7.00 C 8346 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: 5.54 Conformation dependent library (CDL) restraints added in 4.6 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 14 sheets defined 55.1% alpha, 11.0% beta 10 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 71 through 76 removed outlier: 5.138A pdb=" N TYR A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.851A pdb=" N PHE A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.945A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.728A pdb=" N ARG A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 209 removed outlier: 3.512A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 249 through 259 removed outlier: 4.196A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 292 through 317 removed outlier: 3.774A pdb=" N ILE A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.808A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.710A pdb=" N GLN A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.853A pdb=" N THR A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.984A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 611 through 627 Processing helix chain 'A' and resid 639 through 655 Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.562A pdb=" N THR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 removed outlier: 3.535A pdb=" N VAL A 675 " --> pdb=" O GLU A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.783A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 689 " --> pdb=" O MET A 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 682 through 689' Processing helix chain 'A' and resid 696 through 716 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 750 through 756 removed outlier: 4.821A pdb=" N GLY A 753 " --> pdb=" O TRP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 766 Processing helix chain 'A' and resid 767 through 776 Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 802 through 822 Processing helix chain 'A' and resid 824 through 839 removed outlier: 3.573A pdb=" N ASN A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 831 " --> pdb=" O GLN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.825A pdb=" N LEU A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 889 through 903 removed outlier: 4.041A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.151A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 974 removed outlier: 5.601A pdb=" N ILE A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 removed outlier: 3.944A pdb=" N HIS A 993 " --> pdb=" O TRP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.088A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1020 removed outlier: 3.888A pdb=" N MET A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1029 through 1039 removed outlier: 3.635A pdb=" N LYS A1039 " --> pdb=" O HIS A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1058 removed outlier: 3.946A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1108 Processing helix chain 'A' and resid 1109 through 1113 removed outlier: 3.521A pdb=" N GLY A1112 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1155 removed outlier: 3.999A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 4.311A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'A' and resid 1213 through 1228 removed outlier: 3.855A pdb=" N ASP A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1257 through 1266 Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.602A pdb=" N ALA A1284 " --> pdb=" O PRO A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1297 Processing helix chain 'A' and resid 1302 through 1315 removed outlier: 3.521A pdb=" N ILE A1313 " --> pdb=" O TYR A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1356 removed outlier: 3.746A pdb=" N MET A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1368 Processing helix chain 'A' and resid 1369 through 1373 Processing helix chain 'A' and resid 1378 through 1390 Processing helix chain 'A' and resid 1392 through 1397 removed outlier: 3.854A pdb=" N SER A1397 " --> pdb=" O PRO A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1411 removed outlier: 3.581A pdb=" N ARG A1407 " --> pdb=" O HIS A1403 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1448 Processing helix chain 'A' and resid 1449 through 1451 No H-bonds generated for 'chain 'A' and resid 1449 through 1451' Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.955A pdb=" N MET A1463 " --> pdb=" O ASN A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1478 Processing helix chain 'A' and resid 1512 through 1522 Processing helix chain 'A' and resid 1534 through 1546 removed outlier: 3.587A pdb=" N ALA A1543 " --> pdb=" O ASP A1539 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A1545 " --> pdb=" O LEU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1559 removed outlier: 3.625A pdb=" N ASP A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1575 removed outlier: 3.871A pdb=" N ASN A1569 " --> pdb=" O VAL A1565 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A1575 " --> pdb=" O ILE A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1604 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.748A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.674A pdb=" N GLY A 66 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.615A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.615A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AA8, first strand: chain 'A' and resid 921 through 924 removed outlier: 7.529A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1074 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 4.600A pdb=" N TYR A1166 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 6.923A pdb=" N SER A 983 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL A1173 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1178 through 1180 removed outlier: 3.918A pdb=" N PHE A1187 " --> pdb=" O HIS A1190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1338 through 1340 removed outlier: 4.239A pdb=" N MET A1339 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id=AB5, first strand: chain 'A' and resid 1496 through 1503 removed outlier: 3.651A pdb=" N LEU A1502 " --> pdb=" O ARG A1579 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG A1579 " --> pdb=" O LEU A1502 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 6.10 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: 3816 1.33 - 1.45: 2471 1.45 - 1.57: 7294 1.57 - 1.69: 80 1.69 - 1.81: 118 Bond restraints: 13779 Sorted by residual: bond pdb=" N ASN A 14 " pdb=" CA ASN A 14 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.01e+00 bond pdb=" CB ASN A 765 " pdb=" CG ASN A 765 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.32e+00 bond pdb=" CB LYS A 997 " pdb=" CG LYS A 997 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CG GLN A 670 " pdb=" CD GLN A 670 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.97e+00 bond pdb=" CB TRP A1198 " pdb=" CG TRP A1198 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.94e+00 ... (remaining 13774 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.63: 436 105.63 - 112.76: 7352 112.76 - 119.89: 4860 119.89 - 127.03: 5904 127.03 - 134.16: 251 Bond angle restraints: 18803 Sorted by residual: angle pdb=" N GLU A 290 " pdb=" CA GLU A 290 " pdb=" C GLU A 290 " ideal model delta sigma weight residual 111.02 117.20 -6.18 1.25e+00 6.40e-01 2.45e+01 angle pdb=" C THR A 91 " pdb=" CA THR A 91 " pdb=" CB THR A 91 " ideal model delta sigma weight residual 115.89 109.37 6.52 1.32e+00 5.74e-01 2.44e+01 angle pdb=" CA TRP A 520 " pdb=" CB TRP A 520 " pdb=" CG TRP A 520 " ideal model delta sigma weight residual 113.60 121.31 -7.71 1.90e+00 2.77e-01 1.65e+01 angle pdb=" P C G 4 " pdb=" O5' C G 4 " pdb=" C5' C G 4 " ideal model delta sigma weight residual 120.90 126.80 -5.90 1.50e+00 4.44e-01 1.55e+01 angle pdb=" N SER A 96 " pdb=" CA SER A 96 " pdb=" C SER A 96 " ideal model delta sigma weight residual 114.62 110.51 4.11 1.14e+00 7.69e-01 1.30e+01 ... (remaining 18798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.43: 8017 33.43 - 66.85: 332 66.85 - 100.28: 33 100.28 - 133.71: 1 133.71 - 167.14: 1 Dihedral angle restraints: 8384 sinusoidal: 3828 harmonic: 4556 Sorted by residual: dihedral pdb=" O4' U T 22 " pdb=" C1' U T 22 " pdb=" N1 U T 22 " pdb=" C2 U T 22 " ideal model delta sinusoidal sigma weight residual 232.00 64.86 167.14 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" CA LEU A 546 " pdb=" C LEU A 546 " pdb=" N LYS A 547 " pdb=" CA LYS A 547 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" O4' G P 16 " pdb=" C1' G P 16 " pdb=" N9 G P 16 " pdb=" C4 G P 16 " ideal model delta sinusoidal sigma weight residual -106.00 -174.98 68.98 1 1.70e+01 3.46e-03 2.13e+01 ... (remaining 8381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1303 0.038 - 0.075: 594 0.075 - 0.113: 172 0.113 - 0.151: 41 0.151 - 0.189: 4 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CA PRO A1007 " pdb=" N PRO A1007 " pdb=" C PRO A1007 " pdb=" CB PRO A1007 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CB ILE A 479 " pdb=" CA ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CG2 ILE A 479 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" C1' A E 5 " pdb=" O4' A E 5 " pdb=" C2' A E 5 " pdb=" N9 A E 5 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 2111 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 639 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.86e+00 pdb=" C SER A 639 " 0.054 2.00e-02 2.50e+03 pdb=" O SER A 639 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 640 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A1006 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO A1007 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A1007 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1007 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 235 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 236 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.028 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 75 2.55 - 3.14: 10023 3.14 - 3.73: 20569 3.73 - 4.31: 28616 4.31 - 4.90: 47778 Nonbonded interactions: 107061 Sorted by model distance: nonbonded pdb=" OD1 ASP A 985 " pdb="MG MG A2101 " model vdw 1.964 2.170 nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 2.033 2.170 nonbonded pdb=" O LYS A 798 " pdb=" OH TYR A1166 " model vdw 2.108 2.440 nonbonded pdb=" O2' G T 16 " pdb=" OP2 U T 18 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR A1110 " pdb=" OD1 ASP A1141 " model vdw 2.231 2.440 ... (remaining 107056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 2.030 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: 7.310 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 52.130 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.007 0.061 13779 Z= 0.461 Angle : 0.734 9.727 18803 Z= 0.394 Chirality : 0.046 0.189 2114 Planarity : 0.006 0.076 2242 Dihedral : 17.129 167.137 5436 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 6.46 % Allowed : 12.63 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.04 (0.20), residues: 1558 helix: 0.46 (0.18), residues: 771 sheet: -0.30 (0.46), residues: 137 loop : -2.24 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 520 HIS 0.007 0.001 HIS A1246 PHE 0.028 0.002 PHE A 649 TYR 0.017 0.002 TYR A 668 ARG 0.007 0.001 ARG A1579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 139 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6546 (mtm-85) REVERT: A 134 ASN cc_start: 0.7227 (p0) cc_final: 0.6646 (p0) REVERT: A 543 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8695 (tp) REVERT: A 636 LYS cc_start: 0.8476 (mttt) cc_final: 0.8226 (mtmt) REVERT: A 851 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (p) REVERT: A 884 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7148 (tmtt) REVERT: A 919 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7143 (tt) REVERT: A 1205 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 1215 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: A 1217 ASP cc_start: 0.8200 (m-30) cc_final: 0.7795 (m-30) REVERT: A 1290 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7116 (mmp-170) REVERT: A 1414 TYR cc_start: 0.7400 (p90) cc_final: 0.7141 (p90) outliers start: 88 outliers final: 40 residues processed: 216 average time/residue: 1.2401 time to fit residues: 293.1435 Evaluate side-chains 175 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1248 MET Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1582 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 439 ASN A 467 ASN A 765 ASN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 HIS A 915 GLN A1242 GLN A1353 ASN ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13779 Z= 0.155 Angle : 0.530 7.829 18803 Z= 0.281 Chirality : 0.038 0.165 2114 Planarity : 0.004 0.068 2242 Dihedral : 14.658 172.491 2450 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.41 % Allowed : 16.98 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.42 (0.21), residues: 1558 helix: 1.12 (0.19), residues: 756 sheet: 0.39 (0.48), residues: 122 loop : -2.12 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 PHE 0.020 0.001 PHE A1567 TYR 0.014 0.001 TYR A 28 ARG 0.006 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7217 (pp) cc_final: 0.6909 (pp) REVERT: A 93 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6390 (mtm-85) REVERT: A 134 ASN cc_start: 0.7149 (p0) cc_final: 0.6671 (p0) REVERT: A 280 ASP cc_start: 0.8478 (t0) cc_final: 0.8216 (t0) REVERT: A 422 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: A 636 LYS cc_start: 0.8505 (mttt) cc_final: 0.8206 (mtmt) REVERT: A 689 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8057 (mptt) REVERT: A 723 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6958 (ppp80) REVERT: A 919 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6758 (tm) REVERT: A 1215 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: A 1290 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: A 1422 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6468 (ptp90) REVERT: A 1556 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7600 (tp) REVERT: A 1570 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7156 (t80) outliers start: 46 outliers final: 21 residues processed: 178 average time/residue: 1.2883 time to fit residues: 251.4958 Evaluate side-chains 157 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1570 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13779 Z= 0.195 Angle : 0.528 6.644 18803 Z= 0.280 Chirality : 0.039 0.160 2114 Planarity : 0.004 0.063 2242 Dihedral : 14.280 172.017 2405 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.14 % Allowed : 17.85 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.28 (0.21), residues: 1558 helix: 1.26 (0.19), residues: 757 sheet: 0.18 (0.46), residues: 135 loop : -2.08 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.018 0.001 PHE A 649 TYR 0.011 0.001 TYR A1414 ARG 0.008 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 132 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6452 (mtm-85) REVERT: A 134 ASN cc_start: 0.7112 (p0) cc_final: 0.6585 (p0) REVERT: A 280 ASP cc_start: 0.8498 (t0) cc_final: 0.8247 (t0) REVERT: A 636 LYS cc_start: 0.8495 (mttt) cc_final: 0.8206 (mtmt) REVERT: A 689 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8056 (mptt) REVERT: A 919 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7065 (tt) REVERT: A 1215 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.6763 (mt0) REVERT: A 1290 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: A 1422 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6461 (ptp90) REVERT: A 1570 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7208 (t80) outliers start: 56 outliers final: 23 residues processed: 175 average time/residue: 1.3219 time to fit residues: 252.7405 Evaluate side-chains 153 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.0170 chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A1174 ASN ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13779 Z= 0.357 Angle : 0.622 8.038 18803 Z= 0.329 Chirality : 0.043 0.171 2114 Planarity : 0.005 0.066 2242 Dihedral : 14.342 167.580 2399 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.21 % Allowed : 17.92 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.53 (0.21), residues: 1558 helix: 1.03 (0.19), residues: 760 sheet: -0.02 (0.45), residues: 135 loop : -2.16 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 520 HIS 0.006 0.001 HIS A1246 PHE 0.022 0.002 PHE A 649 TYR 0.017 0.002 TYR A1414 ARG 0.007 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 128 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7242 (pp) cc_final: 0.6909 (pp) REVERT: A 93 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6434 (mtm-85) REVERT: A 134 ASN cc_start: 0.7192 (p0) cc_final: 0.6631 (p0) REVERT: A 143 ARG cc_start: 0.7603 (ttm110) cc_final: 0.7263 (ttt180) REVERT: A 636 LYS cc_start: 0.8541 (mttt) cc_final: 0.8245 (mtmt) REVERT: A 689 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8201 (mmtp) REVERT: A 919 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7323 (tt) REVERT: A 1215 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: A 1416 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6698 (mt) outliers start: 57 outliers final: 32 residues processed: 176 average time/residue: 1.3314 time to fit residues: 256.7095 Evaluate side-chains 160 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1204 GLN Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 38 optimal weight: 0.0370 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13779 Z= 0.173 Angle : 0.517 8.550 18803 Z= 0.274 Chirality : 0.038 0.158 2114 Planarity : 0.004 0.062 2242 Dihedral : 14.086 172.363 2394 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.77 % Allowed : 18.72 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1558 helix: 1.29 (0.19), residues: 763 sheet: 0.49 (0.48), residues: 122 loop : -2.09 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.016 0.001 PHE A 649 TYR 0.011 0.001 TYR A 193 ARG 0.004 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6522 (mtm-85) REVERT: A 134 ASN cc_start: 0.7175 (p0) cc_final: 0.6647 (p0) REVERT: A 280 ASP cc_start: 0.8470 (t0) cc_final: 0.8217 (t0) REVERT: A 636 LYS cc_start: 0.8474 (mttt) cc_final: 0.8172 (mtmt) REVERT: A 689 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8060 (mptt) REVERT: A 919 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7068 (tt) REVERT: A 1215 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.6367 (mm-40) REVERT: A 1264 MET cc_start: 0.8230 (ttm) cc_final: 0.7988 (ptt) REVERT: A 1290 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7178 (mmp-170) REVERT: A 1416 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6552 (mt) REVERT: A 1422 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6327 (ptp90) REVERT: A 1447 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7434 (tp) REVERT: A 1570 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7222 (t80) outliers start: 51 outliers final: 29 residues processed: 176 average time/residue: 1.2817 time to fit residues: 246.8094 Evaluate side-chains 165 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 0.0040 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13779 Z= 0.355 Angle : 0.620 9.419 18803 Z= 0.327 Chirality : 0.043 0.170 2114 Planarity : 0.005 0.063 2242 Dihedral : 14.223 168.174 2394 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.35 % Allowed : 18.65 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.51 (0.21), residues: 1558 helix: 1.06 (0.19), residues: 760 sheet: -0.02 (0.45), residues: 135 loop : -2.16 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.022 0.002 PHE A 649 TYR 0.016 0.002 TYR A1414 ARG 0.006 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 128 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7200 (pp) cc_final: 0.6874 (pp) REVERT: A 67 LEU cc_start: 0.7638 (tt) cc_final: 0.7424 (tt) REVERT: A 93 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6508 (mtm-85) REVERT: A 134 ASN cc_start: 0.7205 (p0) cc_final: 0.6642 (p0) REVERT: A 143 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7265 (ttt180) REVERT: A 636 LYS cc_start: 0.8550 (mttt) cc_final: 0.8256 (mtmt) REVERT: A 689 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8206 (mmtp) REVERT: A 1215 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.6545 (mm-40) REVERT: A 1290 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7200 (mmp-170) REVERT: A 1416 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6742 (mt) REVERT: A 1447 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7523 (tp) REVERT: A 1570 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7360 (t80) outliers start: 59 outliers final: 33 residues processed: 176 average time/residue: 1.2825 time to fit residues: 246.5118 Evaluate side-chains 167 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1248 MET Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13779 Z= 0.217 Angle : 0.560 13.115 18803 Z= 0.291 Chirality : 0.039 0.154 2114 Planarity : 0.004 0.063 2242 Dihedral : 14.083 170.903 2392 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.77 % Allowed : 19.59 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.29 (0.21), residues: 1558 helix: 1.27 (0.19), residues: 759 sheet: 0.44 (0.47), residues: 122 loop : -2.12 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 520 HIS 0.005 0.001 HIS A1246 PHE 0.018 0.001 PHE A 649 TYR 0.013 0.001 TYR A1414 ARG 0.005 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7664 (tt) cc_final: 0.7430 (tt) REVERT: A 93 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6495 (mtm-85) REVERT: A 134 ASN cc_start: 0.7209 (p0) cc_final: 0.6659 (p0) REVERT: A 443 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: A 636 LYS cc_start: 0.8526 (mttt) cc_final: 0.8238 (mtmt) REVERT: A 689 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8094 (mptt) REVERT: A 1215 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.6384 (mm-40) REVERT: A 1290 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7183 (mmp-170) REVERT: A 1416 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6636 (mt) REVERT: A 1422 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6192 (ptp90) REVERT: A 1447 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7465 (tp) REVERT: A 1505 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.3928 (tm-30) outliers start: 51 outliers final: 31 residues processed: 174 average time/residue: 1.3501 time to fit residues: 256.3172 Evaluate side-chains 163 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13779 Z= 0.229 Angle : 0.575 13.368 18803 Z= 0.297 Chirality : 0.040 0.152 2114 Planarity : 0.004 0.062 2242 Dihedral : 14.053 171.122 2392 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.63 % Allowed : 19.74 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.28 (0.21), residues: 1558 helix: 1.27 (0.19), residues: 760 sheet: 0.14 (0.45), residues: 135 loop : -2.10 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1538 HIS 0.005 0.001 HIS A1246 PHE 0.028 0.002 PHE A1567 TYR 0.016 0.001 TYR A1414 ARG 0.006 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7168 (pp) cc_final: 0.6833 (pp) REVERT: A 67 LEU cc_start: 0.7696 (tt) cc_final: 0.7450 (tt) REVERT: A 93 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6542 (mtm-85) REVERT: A 134 ASN cc_start: 0.7175 (p0) cc_final: 0.6633 (p0) REVERT: A 214 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.7004 (mm) REVERT: A 443 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: A 636 LYS cc_start: 0.8525 (mttt) cc_final: 0.8234 (mtmt) REVERT: A 689 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8088 (mptt) REVERT: A 1290 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7201 (mmp-170) REVERT: A 1416 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6587 (mt) REVERT: A 1447 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7462 (tp) REVERT: A 1505 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.3990 (tm-30) outliers start: 49 outliers final: 34 residues processed: 168 average time/residue: 1.2950 time to fit residues: 237.5051 Evaluate side-chains 166 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1505 GLU Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13779 Z= 0.360 Angle : 0.659 14.601 18803 Z= 0.342 Chirality : 0.043 0.304 2114 Planarity : 0.005 0.063 2242 Dihedral : 14.133 167.982 2389 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.63 % Allowed : 19.67 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.54 (0.21), residues: 1558 helix: 1.05 (0.19), residues: 760 sheet: -0.05 (0.45), residues: 135 loop : -2.19 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1538 HIS 0.005 0.001 HIS A1246 PHE 0.021 0.002 PHE A 649 TYR 0.020 0.002 TYR A1414 ARG 0.008 0.000 ARG A1557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 123 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7183 (pp) cc_final: 0.6836 (pp) REVERT: A 67 LEU cc_start: 0.7743 (tt) cc_final: 0.7515 (tt) REVERT: A 93 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6516 (mtm-85) REVERT: A 134 ASN cc_start: 0.7198 (p0) cc_final: 0.6654 (p0) REVERT: A 143 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7270 (ttt180) REVERT: A 214 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7021 (mm) REVERT: A 443 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: A 636 LYS cc_start: 0.8545 (mttt) cc_final: 0.8262 (mtmt) REVERT: A 689 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8125 (mptt) REVERT: A 1290 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7210 (mmp-170) REVERT: A 1416 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6693 (mt) REVERT: A 1447 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7569 (tp) outliers start: 49 outliers final: 35 residues processed: 163 average time/residue: 1.3131 time to fit residues: 233.5145 Evaluate side-chains 164 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 104 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13779 Z= 0.250 Angle : 0.599 14.204 18803 Z= 0.310 Chirality : 0.041 0.254 2114 Planarity : 0.004 0.063 2242 Dihedral : 14.027 170.092 2389 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.48 % Allowed : 19.81 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.35 (0.21), residues: 1558 helix: 1.19 (0.19), residues: 764 sheet: 0.40 (0.47), residues: 122 loop : -2.15 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1538 HIS 0.005 0.001 HIS A1246 PHE 0.031 0.002 PHE A1567 TYR 0.019 0.002 TYR A1414 ARG 0.009 0.000 ARG A1557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 126 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.7143 (pp) cc_final: 0.6777 (pp) REVERT: A 67 LEU cc_start: 0.7735 (tt) cc_final: 0.7509 (tt) REVERT: A 93 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6470 (mtm-85) REVERT: A 134 ASN cc_start: 0.7182 (p0) cc_final: 0.6631 (p0) REVERT: A 214 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7024 (mm) REVERT: A 443 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: A 636 LYS cc_start: 0.8543 (mttt) cc_final: 0.8252 (mtmt) REVERT: A 689 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8094 (mptt) REVERT: A 1290 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7189 (mmp-170) REVERT: A 1304 ARG cc_start: 0.6146 (tpt170) cc_final: 0.5802 (tpt170) REVERT: A 1416 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6610 (mt) REVERT: A 1447 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7563 (tp) outliers start: 47 outliers final: 35 residues processed: 166 average time/residue: 1.3005 time to fit residues: 236.5114 Evaluate side-chains 166 residues out of total 1374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1459 ASN Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.0170 chunk 110 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.143910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111064 restraints weight = 39379.900| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.89 r_work: 0.3214 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 13779 Z= 0.154 Angle : 0.543 13.859 18803 Z= 0.279 Chirality : 0.038 0.151 2114 Planarity : 0.004 0.062 2242 Dihedral : 13.819 175.185 2389 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.25 % Allowed : 21.19 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.05 (0.22), residues: 1558 helix: 1.42 (0.19), residues: 769 sheet: 0.39 (0.46), residues: 135 loop : -2.00 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 520 HIS 0.004 0.001 HIS A1246 PHE 0.019 0.001 PHE A 934 TYR 0.013 0.001 TYR A 193 ARG 0.009 0.000 ARG A1557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4585.06 seconds wall clock time: 81 minutes 2.72 seconds (4862.72 seconds total)