Starting phenix.real_space_refine on Wed Feb 14 21:55:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci5_16670/02_2024/8ci5_16670.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci5_16670/02_2024/8ci5_16670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci5_16670/02_2024/8ci5_16670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci5_16670/02_2024/8ci5_16670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci5_16670/02_2024/8ci5_16670.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci5_16670/02_2024/8ci5_16670.pdb" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 49 5.16 5 C 6629 2.51 5 N 1738 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 592": "OD1" <-> "OD2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A ARG 881": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A GLU 907": "OE1" <-> "OE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1000": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1238": "OE1" <-> "OE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "A TYR 1307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1449": "OD1" <-> "OD2" Residue "A PHE 1451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1517": "OD1" <-> "OD2" Residue "A ASP 1524": "OD1" <-> "OD2" Residue "A GLU 1546": "OE1" <-> "OE2" Residue "A TYR 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1584": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10365 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10128 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1258, 10124 Classifications: {'peptide': 1258} Link IDs: {'PTRANS': 41, 'TRANS': 1216} Chain breaks: 15 Conformer: "B" Number of residues, atoms: 1258, 10124 Classifications: {'peptide': 1258} Link IDs: {'PTRANS': 41, 'TRANS': 1216} Chain breaks: 15 bond proxies already assigned to first conformer: 10337 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A1047 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1047 " occ=0.50 Time building chain proxies: 10.63, per 1000 atoms: 1.03 Number of scatterers: 10365 At special positions: 0 Unit cell: (101.15, 88.4, 125.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 11 15.00 O 1938 8.00 N 1738 7.00 C 6629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 3.6 seconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 57.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.760A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.961A pdb=" N VAL A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.821A pdb=" N ILE A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 4.031A pdb=" N LEU A 378 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.694A pdb=" N LYS A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 426 Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.690A pdb=" N HIS A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'A' and resid 573 through 594 Processing helix chain 'A' and resid 598 through 616 removed outlier: 3.681A pdb=" N GLN A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 635 removed outlier: 3.587A pdb=" N CYS A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 3.611A pdb=" N THR A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.667A pdb=" N PHE A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 675 removed outlier: 3.754A pdb=" N VAL A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 727 removed outlier: 4.347A pdb=" N LEU A 717 " --> pdb=" O HIS A 713 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 742 through 761 removed outlier: 4.583A pdb=" N THR A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 removed outlier: 3.523A pdb=" N MET A 765 " --> pdb=" O GLY A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 787 through 803 Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.579A pdb=" N MET A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 3.923A pdb=" N SER A 830 " --> pdb=" O ARG A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 removed outlier: 3.567A pdb=" N ASN A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 899 through 918 Processing helix chain 'A' and resid 932 through 947 removed outlier: 3.661A pdb=" N ALA A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 992 removed outlier: 4.451A pdb=" N ARG A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1011 Processing helix chain 'A' and resid 1021 through 1030 removed outlier: 3.515A pdb=" N ASP A1029 " --> pdb=" O HIS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1045 removed outlier: 3.611A pdb=" N ASP A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A1045 " --> pdb=" O PHE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1083 Processing helix chain 'A' and resid 1115 through 1127 removed outlier: 3.668A pdb=" N ALA A1127 " --> pdb=" O GLN A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1135 removed outlier: 3.642A pdb=" N ALA A1134 " --> pdb=" O HIS A1131 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A1135 " --> pdb=" O TRP A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1154 Processing helix chain 'A' and resid 1186 through 1192 removed outlier: 3.521A pdb=" N LEU A1190 " --> pdb=" O PHE A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1219 removed outlier: 3.654A pdb=" N ASP A1205 " --> pdb=" O GLY A1201 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A1213 " --> pdb=" O ALA A1209 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1219 " --> pdb=" O LYS A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1242 Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1283 through 1301 removed outlier: 3.905A pdb=" N LYS A1287 " --> pdb=" O GLY A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1318 removed outlier: 3.617A pdb=" N LEU A1318 " --> pdb=" O PHE A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1366 Processing helix chain 'A' and resid 1367 through 1371 removed outlier: 3.707A pdb=" N ASP A1370 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1390 removed outlier: 3.534A pdb=" N LEU A1380 " --> pdb=" O GLY A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1398 Processing helix chain 'A' and resid 1401 through 1408 removed outlier: 4.240A pdb=" N LEU A1405 " --> pdb=" O SER A1401 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A1406 " --> pdb=" O PRO A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1440 Processing helix chain 'A' and resid 1449 through 1456 Processing helix chain 'A' and resid 1504 through 1513 removed outlier: 4.239A pdb=" N TYR A1512 " --> pdb=" O ILE A1508 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1525 Processing helix chain 'A' and resid 1531 through 1547 removed outlier: 4.108A pdb=" N GLN A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1558 removed outlier: 4.200A pdb=" N LEU A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A1558 " --> pdb=" O PRO A1554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1553 through 1558' Processing helix chain 'A' and resid 1560 through 1567 removed outlier: 3.534A pdb=" N LEU A1564 " --> pdb=" O ILE A1560 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A1567 " --> pdb=" O LEU A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1593 removed outlier: 3.774A pdb=" N SER A1588 " --> pdb=" O GLU A1584 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A1589 " --> pdb=" O SER A1585 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.700A pdb=" N THR A1164 " --> pdb=" O SER A 971 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A1105 " --> pdb=" O MET A 968 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A1101 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A1106 " --> pdb=" O PHE A1091 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 284 removed outlier: 5.830A pdb=" N LYS A 283 " --> pdb=" O SER A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298 removed outlier: 4.158A pdb=" N ILE A 536 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 504 removed outlier: 5.174A pdb=" N THR A 530 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 504 removed outlier: 3.570A pdb=" N ILE A 563 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 898 removed outlier: 7.082A pdb=" N ALA A 880 " --> pdb=" O PHE A1019 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 954 Processing sheet with id=AA9, first strand: chain 'A' and resid 964 through 965 Processing sheet with id=AB1, first strand: chain 'A' and resid 1170 through 1172 Processing sheet with id=AB2, first strand: chain 'A' and resid 1418 through 1420 Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1491 508 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2288 1.33 - 1.45: 2508 1.45 - 1.57: 5715 1.57 - 1.69: 22 1.69 - 1.81: 79 Bond restraints: 10612 Sorted by residual: bond pdb=" CA SER A1193 " pdb=" C SER A1193 " ideal model delta sigma weight residual 1.522 1.462 0.061 1.34e-02 5.57e+03 2.04e+01 bond pdb=" C ILE A1264 " pdb=" N PRO A1265 " ideal model delta sigma weight residual 1.337 1.366 -0.030 9.80e-03 1.04e+04 9.14e+00 bond pdb=" N GLN A1059 " pdb=" CA GLN A1059 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.03e+00 bond pdb=" C ALA A 845 " pdb=" N ALA A 846 " ideal model delta sigma weight residual 1.334 1.294 0.040 1.52e-02 4.33e+03 6.89e+00 bond pdb=" CA LEU A 464 " pdb=" C LEU A 464 " ideal model delta sigma weight residual 1.524 1.506 0.018 7.00e-03 2.04e+04 6.89e+00 ... (remaining 10607 not shown) Histogram of bond angle deviations from ideal: 95.96 - 104.29: 181 104.29 - 112.61: 5455 112.61 - 120.94: 5664 120.94 - 129.27: 2999 129.27 - 137.59: 87 Bond angle restraints: 14386 Sorted by residual: angle pdb=" CA PRO A1391 " pdb=" N PRO A1391 " pdb=" CD PRO A1391 " ideal model delta sigma weight residual 112.00 100.12 11.88 1.40e+00 5.10e-01 7.20e+01 angle pdb=" N VAL A1049 " pdb=" CA VAL A1049 " pdb=" C VAL A1049 " ideal model delta sigma weight residual 113.47 106.24 7.23 1.01e+00 9.80e-01 5.13e+01 angle pdb=" N VAL A 277 " pdb=" CA VAL A 277 " pdb=" C VAL A 277 " ideal model delta sigma weight residual 111.77 105.89 5.88 1.04e+00 9.25e-01 3.19e+01 angle pdb=" C SER A1531 " pdb=" N LEU A1532 " pdb=" CA LEU A1532 " ideal model delta sigma weight residual 120.44 126.63 -6.19 1.30e+00 5.92e-01 2.27e+01 angle pdb=" N VAL A1252 " pdb=" CA VAL A1252 " pdb=" C VAL A1252 " ideal model delta sigma weight residual 113.07 106.88 6.19 1.37e+00 5.33e-01 2.04e+01 ... (remaining 14381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.94: 6034 26.94 - 53.87: 266 53.87 - 80.81: 41 80.81 - 107.75: 6 107.75 - 134.68: 1 Dihedral angle restraints: 6348 sinusoidal: 2658 harmonic: 3690 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 65.32 134.68 1 1.50e+01 4.44e-03 7.27e+01 dihedral pdb=" CA SER A 926 " pdb=" C SER A 926 " pdb=" N TYR A 927 " pdb=" CA TYR A 927 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ARG A 893 " pdb=" C ARG A 893 " pdb=" N GLY A 894 " pdb=" CA GLY A 894 " ideal model delta harmonic sigma weight residual 180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 6345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1262 0.078 - 0.157: 312 0.157 - 0.235: 33 0.235 - 0.314: 2 0.314 - 0.392: 2 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CB VAL A1135 " pdb=" CA VAL A1135 " pdb=" CG1 VAL A1135 " pdb=" CG2 VAL A1135 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PRO A1391 " pdb=" N PRO A1391 " pdb=" C PRO A1391 " pdb=" CB PRO A1391 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB VAL A1394 " pdb=" CA VAL A1394 " pdb=" CG1 VAL A1394 " pdb=" CG2 VAL A1394 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1608 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1292 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C GLN A1292 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN A1292 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA A1293 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1390 " -0.053 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO A1391 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1391 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1391 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1297 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C TYR A1297 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A1297 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS A1298 " -0.017 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1227 2.73 - 3.27: 9735 3.27 - 3.82: 16550 3.82 - 4.36: 20800 4.36 - 4.90: 35442 Nonbonded interactions: 83754 Sorted by model distance: nonbonded pdb=" O ILE A 408 " pdb=" NE2 GLN A 414 " model vdw 2.190 2.520 nonbonded pdb=" OE2 GLU A 739 " pdb=" OG SER A1021 " model vdw 2.211 2.440 nonbonded pdb=" O GLU A1580 " pdb=" OG SER A1585 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR A 913 " pdb=" OG1 THR A 990 " model vdw 2.233 2.440 nonbonded pdb=" O LEU A1119 " pdb=" OG SER A1122 " model vdw 2.242 2.440 ... (remaining 83749 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=0.50 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: 3.870 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: 9.840 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 38.910 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.014 0.116 10612 Z= 0.892 Angle : 1.190 12.820 14386 Z= 0.665 Chirality : 0.067 0.392 1611 Planarity : 0.008 0.073 1772 Dihedral : 15.440 134.683 3960 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.32 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.20), residues: 1229 helix: -2.14 (0.16), residues: 658 sheet: -2.93 (0.44), residues: 105 loop : -2.94 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A1424 HIS 0.011 0.003 HIS A 733 PHE 0.048 0.005 PHE A1437 TYR 0.039 0.004 TYR A 504 ARG 0.029 0.002 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.309 Fit side-chains REVERT: A 345 ASN cc_start: 0.7830 (t0) cc_final: 0.7598 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2644 time to fit residues: 43.4926 Evaluate side-chains 101 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A 478 HIS A 626 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 ASN A1404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10612 Z= 0.179 Angle : 0.558 7.935 14386 Z= 0.298 Chirality : 0.040 0.160 1611 Planarity : 0.005 0.056 1772 Dihedral : 9.096 133.118 1522 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 0.27 % Allowed : 3.96 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.22), residues: 1229 helix: -0.33 (0.19), residues: 661 sheet: -1.99 (0.48), residues: 105 loop : -2.29 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 474 HIS 0.004 0.001 HIS A 733 PHE 0.023 0.002 PHE A1186 TYR 0.015 0.001 TYR A 504 ARG 0.003 0.000 ARG A1571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.366 Fit side-chains REVERT: A 337 MET cc_start: 0.8696 (mtp) cc_final: 0.8479 (mtp) outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.2878 time to fit residues: 48.6793 Evaluate side-chains 109 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1133 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10612 Z= 0.198 Angle : 0.530 7.500 14386 Z= 0.279 Chirality : 0.040 0.167 1611 Planarity : 0.004 0.057 1772 Dihedral : 8.733 132.345 1522 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 0.36 % Allowed : 6.29 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1229 helix: 0.48 (0.20), residues: 661 sheet: -1.42 (0.50), residues: 100 loop : -1.99 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 474 HIS 0.004 0.001 HIS A 733 PHE 0.021 0.002 PHE A1186 TYR 0.014 0.001 TYR A 504 ARG 0.004 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.101 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 116 average time/residue: 0.2723 time to fit residues: 43.2264 Evaluate side-chains 110 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1215 LYS Chi-restraints excluded: chain A residue 1532 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10612 Z= 0.187 Angle : 0.509 7.279 14386 Z= 0.265 Chirality : 0.040 0.154 1611 Planarity : 0.004 0.058 1772 Dihedral : 8.592 130.734 1522 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 0.63 % Allowed : 7.55 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1229 helix: 0.91 (0.20), residues: 663 sheet: -1.11 (0.51), residues: 100 loop : -1.81 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 474 HIS 0.004 0.001 HIS A 733 PHE 0.019 0.002 PHE A1186 TYR 0.013 0.001 TYR A1383 ARG 0.003 0.000 ARG A1301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.121 Fit side-chains REVERT: A 1173 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5585 (pp) outliers start: 7 outliers final: 3 residues processed: 115 average time/residue: 0.2739 time to fit residues: 42.4561 Evaluate side-chains 110 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1215 LYS Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 0.0020 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10612 Z= 0.170 Angle : 0.496 8.165 14386 Z= 0.257 Chirality : 0.039 0.155 1611 Planarity : 0.004 0.057 1772 Dihedral : 8.527 129.897 1522 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 0.90 % Allowed : 8.81 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1229 helix: 1.15 (0.20), residues: 664 sheet: -1.01 (0.52), residues: 94 loop : -1.61 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 474 HIS 0.004 0.001 HIS A 733 PHE 0.019 0.002 PHE A1186 TYR 0.023 0.001 TYR A 927 ARG 0.003 0.000 ARG A1301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.143 Fit side-chains REVERT: A 1173 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5590 (pp) outliers start: 10 outliers final: 6 residues processed: 120 average time/residue: 0.3179 time to fit residues: 51.5734 Evaluate side-chains 113 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1215 LYS Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10612 Z= 0.191 Angle : 0.508 7.620 14386 Z= 0.264 Chirality : 0.040 0.157 1611 Planarity : 0.004 0.058 1772 Dihedral : 8.514 128.199 1522 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 0.99 % Allowed : 9.17 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1229 helix: 1.24 (0.20), residues: 664 sheet: -0.92 (0.53), residues: 94 loop : -1.50 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 474 HIS 0.004 0.001 HIS A 733 PHE 0.020 0.002 PHE A1186 TYR 0.019 0.001 TYR A 927 ARG 0.004 0.000 ARG A1428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.172 Fit side-chains REVERT: A 1173 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5617 (pp) outliers start: 11 outliers final: 6 residues processed: 118 average time/residue: 0.2621 time to fit residues: 42.8771 Evaluate side-chains 116 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.0040 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10612 Z= 0.235 Angle : 0.536 8.013 14386 Z= 0.278 Chirality : 0.041 0.159 1611 Planarity : 0.004 0.060 1772 Dihedral : 8.539 126.020 1522 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 0.99 % Allowed : 9.35 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1229 helix: 1.20 (0.20), residues: 664 sheet: -0.83 (0.51), residues: 100 loop : -1.51 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 474 HIS 0.004 0.001 HIS A 733 PHE 0.020 0.002 PHE A1186 TYR 0.020 0.001 TYR A 927 ARG 0.003 0.000 ARG A1428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.346 Fit side-chains REVERT: A 1120 TYR cc_start: 0.7762 (t80) cc_final: 0.7515 (t80) REVERT: A 1173 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5546 (pp) REVERT: A 1399 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5199 (ttt) outliers start: 11 outliers final: 8 residues processed: 114 average time/residue: 0.2724 time to fit residues: 42.6448 Evaluate side-chains 118 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10612 Z= 0.185 Angle : 0.510 8.336 14386 Z= 0.263 Chirality : 0.040 0.157 1611 Planarity : 0.004 0.061 1772 Dihedral : 8.477 125.200 1522 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 0.90 % Allowed : 9.08 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1229 helix: 1.32 (0.20), residues: 664 sheet: -0.80 (0.54), residues: 94 loop : -1.41 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 474 HIS 0.003 0.001 HIS A 743 PHE 0.020 0.002 PHE A1437 TYR 0.017 0.001 TYR A 927 ARG 0.003 0.000 ARG A1428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.311 Fit side-chains REVERT: A 1120 TYR cc_start: 0.7779 (t80) cc_final: 0.7499 (t80) REVERT: A 1173 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5565 (pp) REVERT: A 1399 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5243 (ttt) REVERT: A 1555 GLU cc_start: 0.7203 (mp0) cc_final: 0.6892 (mp0) outliers start: 10 outliers final: 6 residues processed: 120 average time/residue: 0.2683 time to fit residues: 44.3790 Evaluate side-chains 117 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10612 Z= 0.212 Angle : 0.526 8.374 14386 Z= 0.272 Chirality : 0.040 0.159 1611 Planarity : 0.004 0.061 1772 Dihedral : 8.491 123.791 1522 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.72 % Allowed : 9.35 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1229 helix: 1.34 (0.20), residues: 665 sheet: -0.77 (0.51), residues: 100 loop : -1.43 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 474 HIS 0.004 0.001 HIS A 743 PHE 0.020 0.002 PHE A1186 TYR 0.013 0.001 TYR A1383 ARG 0.003 0.000 ARG A1428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.223 Fit side-chains REVERT: A 927 TYR cc_start: 0.5733 (t80) cc_final: 0.5512 (t80) REVERT: A 1120 TYR cc_start: 0.7764 (t80) cc_final: 0.7504 (t80) REVERT: A 1173 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5584 (pp) REVERT: A 1399 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5168 (ttt) REVERT: A 1555 GLU cc_start: 0.7192 (mp0) cc_final: 0.6897 (mp0) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.2929 time to fit residues: 45.4936 Evaluate side-chains 118 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10612 Z= 0.229 Angle : 0.539 8.296 14386 Z= 0.279 Chirality : 0.041 0.159 1611 Planarity : 0.004 0.060 1772 Dihedral : 8.508 121.902 1522 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 0.72 % Allowed : 9.35 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1229 helix: 1.32 (0.20), residues: 664 sheet: -0.75 (0.52), residues: 100 loop : -1.45 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 474 HIS 0.004 0.001 HIS A 743 PHE 0.020 0.002 PHE A1186 TYR 0.013 0.001 TYR A1383 ARG 0.003 0.000 ARG A1428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.324 Fit side-chains REVERT: A 1120 TYR cc_start: 0.7776 (t80) cc_final: 0.7453 (t80) REVERT: A 1173 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5579 (pp) REVERT: A 1399 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.5193 (ttt) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.2804 time to fit residues: 44.0049 Evaluate side-chains 115 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.0370 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102595 restraints weight = 15918.744| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.75 r_work: 0.3141 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10612 Z= 0.123 Angle : 0.486 9.090 14386 Z= 0.248 Chirality : 0.038 0.153 1611 Planarity : 0.004 0.060 1772 Dihedral : 8.347 122.904 1522 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 0.36 % Allowed : 9.89 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1229 helix: 1.71 (0.20), residues: 661 sheet: -0.71 (0.53), residues: 94 loop : -1.31 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 946 HIS 0.003 0.001 HIS A 743 PHE 0.020 0.001 PHE A1437 TYR 0.014 0.001 TYR A 913 ARG 0.003 0.000 ARG A1428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.95 seconds wall clock time: 45 minutes 27.09 seconds (2727.09 seconds total)