Starting phenix.real_space_refine on Fri Oct 30 17:36:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/37ht_78192/10_2026/37ht_78192_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/37ht_78192/10_2026/37ht_78192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/37ht_78192/10_2026/37ht_78192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/37ht_78192/10_2026/37ht_78192.map" model { file = "/net/cci-nas-00/data/ceres_data/37ht_78192/10_2026/37ht_78192_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/37ht_78192/10_2026/37ht_78192_trim.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.032 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 11736 2.51 5 N 3004 2.21 5 O 3360 1.98 5 H 18216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36406 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 18171 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 39, 'TRANS': 1066} Chain breaks: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 38.55, per 1000 atoms: 1.06 Number of scatterers: 36406 At special positions: 0 Unit cell: (131.34, 186.78, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 82 16.00 P 6 15.00 Mg 2 11.99 O 3360 8.00 N 3004 7.00 C 11736 6.00 H 18216 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4232 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 61.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.661A pdb=" N LYS A 426 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 428 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 517 through 529 removed outlier: 3.509A pdb=" N VAL A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 568 removed outlier: 3.502A pdb=" N GLU A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.666A pdb=" N GLY A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.774A pdb=" N PHE A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 742 through 754 removed outlier: 3.816A pdb=" N LEU A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 804 through 822 removed outlier: 4.389A pdb=" N TYR A 808 " --> pdb=" O GLN A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 858 through 876 removed outlier: 3.838A pdb=" N GLU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 881 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 893 through 906 removed outlier: 3.719A pdb=" N ILE A 897 " --> pdb=" O ASN A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 928 Processing helix chain 'A' and resid 935 through 942 Processing helix chain 'A' and resid 956 through 961 Processing helix chain 'A' and resid 962 through 965 removed outlier: 3.511A pdb=" N THR A 965 " --> pdb=" O THR A 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 962 through 965' Processing helix chain 'A' and resid 985 through 1000 Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1014 through 1018 Processing helix chain 'A' and resid 1023 through 1036 removed outlier: 3.513A pdb=" N PHE A1027 " --> pdb=" O GLY A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1063 Processing helix chain 'A' and resid 1064 through 1078 Processing helix chain 'A' and resid 1081 through 1095 removed outlier: 3.927A pdb=" N CYS A1085 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1113 removed outlier: 3.569A pdb=" N ALA A1102 " --> pdb=" O ASP A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1138 removed outlier: 3.660A pdb=" N SER A1120 " --> pdb=" O ASN A1116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A1130 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1174 removed outlier: 3.513A pdb=" N GLU A1174 " --> pdb=" O SER A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1212 removed outlier: 3.555A pdb=" N GLN A1198 " --> pdb=" O ILE A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 6.138A pdb=" N PHE A1216 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A1218 " --> pdb=" O PRO A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1244 through 1252 removed outlier: 4.029A pdb=" N ASN A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1258 Processing helix chain 'A' and resid 1259 through 1277 Processing helix chain 'A' and resid 1285 through 1308 removed outlier: 3.856A pdb=" N GLU A1289 " --> pdb=" O LYS A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1339 Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1375 removed outlier: 4.054A pdb=" N SER A1360 " --> pdb=" O GLU A1356 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A1375 " --> pdb=" O PHE A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1399 removed outlier: 3.722A pdb=" N LYS A1385 " --> pdb=" O GLN A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1420 Processing helix chain 'A' and resid 1429 through 1439 Processing helix chain 'A' and resid 1453 through 1468 removed outlier: 3.504A pdb=" N GLN A1458 " --> pdb=" O LYS A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1490 Processing helix chain 'A' and resid 1495 through 1501 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.515A pdb=" N GLN A1524 " --> pdb=" O GLU A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1538 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.661A pdb=" N LYS B 426 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 428 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 517 through 529 removed outlier: 3.509A pdb=" N VAL B 521 " --> pdb=" O ARG B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.502A pdb=" N GLU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 642 through 647 Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.666A pdb=" N GLY B 686 " --> pdb=" O ASP B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.774A pdb=" N PHE B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.816A pdb=" N LEU B 746 " --> pdb=" O GLY B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 804 through 822 removed outlier: 4.389A pdb=" N TYR B 808 " --> pdb=" O GLN B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 845 Processing helix chain 'B' and resid 858 through 876 removed outlier: 3.838A pdb=" N GLU B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 881 Processing helix chain 'B' and resid 882 through 890 Processing helix chain 'B' and resid 893 through 906 removed outlier: 3.719A pdb=" N ILE B 897 " --> pdb=" O ASN B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 928 Processing helix chain 'B' and resid 935 through 942 Processing helix chain 'B' and resid 956 through 961 Processing helix chain 'B' and resid 962 through 965 removed outlier: 3.511A pdb=" N THR B 965 " --> pdb=" O THR B 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 985 through 1000 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1014 through 1018 Processing helix chain 'B' and resid 1023 through 1036 removed outlier: 3.513A pdb=" N PHE B1027 " --> pdb=" O GLY B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1063 Processing helix chain 'B' and resid 1064 through 1078 Processing helix chain 'B' and resid 1081 through 1095 removed outlier: 3.927A pdb=" N CYS B1085 " --> pdb=" O ASN B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1113 removed outlier: 3.569A pdb=" N ALA B1102 " --> pdb=" O ASP B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1138 removed outlier: 3.660A pdb=" N SER B1120 " --> pdb=" O ASN B1116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B1130 " --> pdb=" O VAL B1126 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B1131 " --> pdb=" O TYR B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1174 removed outlier: 3.513A pdb=" N GLU B1174 " --> pdb=" O SER B1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1212 removed outlier: 3.555A pdb=" N GLN B1198 " --> pdb=" O ILE B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1218 removed outlier: 6.138A pdb=" N PHE B1216 " --> pdb=" O LEU B1213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B1218 " --> pdb=" O PRO B1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1232 Processing helix chain 'B' and resid 1244 through 1252 removed outlier: 4.029A pdb=" N ASN B1252 " --> pdb=" O LEU B1248 " (cutoff:3.500A) Processing helix chain 'B' and resid 1253 through 1258 Processing helix chain 'B' and resid 1259 through 1277 Processing helix chain 'B' and resid 1285 through 1308 removed outlier: 3.856A pdb=" N GLU B1289 " --> pdb=" O LYS B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1339 Processing helix chain 'B' and resid 1343 through 1349 Processing helix chain 'B' and resid 1350 through 1352 No H-bonds generated for 'chain 'B' and resid 1350 through 1352' Processing helix chain 'B' and resid 1354 through 1375 removed outlier: 4.054A pdb=" N SER B1360 " --> pdb=" O GLU B1356 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B1375 " --> pdb=" O PHE B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1399 removed outlier: 3.722A pdb=" N LYS B1385 " --> pdb=" O GLN B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1407 through 1420 Processing helix chain 'B' and resid 1429 through 1439 Processing helix chain 'B' and resid 1453 through 1468 removed outlier: 3.504A pdb=" N GLN B1458 " --> pdb=" O LYS B1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 1487 through 1490 Processing helix chain 'B' and resid 1495 through 1501 Processing helix chain 'B' and resid 1520 through 1525 removed outlier: 3.515A pdb=" N GLN B1524 " --> pdb=" O GLU B1520 " (cutoff:3.500A) Processing helix chain 'B' and resid 1535 through 1538 Processing sheet with id=1, first strand: chain 'A' and resid 462 through 464 removed outlier: 6.248A pdb=" N ASN A 462 " --> pdb=" O TRP A 491 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE A 493 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS A 464 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR A 413 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU A 440 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 415 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN A 412 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL A 542 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 414 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU A 544 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 416 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU A 574 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 541 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A 576 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 543 " --> pdb=" O ILE A 576 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 631 through 632 Processing sheet with id=3, first strand: chain 'A' and resid 653 through 654 removed outlier: 6.477A pdb=" N VAL A 794 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU A 833 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 796 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N CYS A 835 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 798 " --> pdb=" O CYS A 835 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ARG A 837 " --> pdb=" O VAL A 798 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS A 731 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN A 834 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 733 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET A 836 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A 735 " --> pdb=" O MET A 836 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL A 853 " --> pdb=" O HIS A 734 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR A 736 " --> pdb=" O VAL A 853 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 933 through 934 Processing sheet with id=5, first strand: chain 'A' and resid 1278 through 1280 Processing sheet with id=6, first strand: chain 'A' and resid 1492 through 1494 removed outlier: 3.798A pdb=" N PHE A1481 " --> pdb=" O PHE A1576 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A1574 " --> pdb=" O LEU A1483 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 1492 through 1494 removed outlier: 3.798A pdb=" N PHE A1481 " --> pdb=" O PHE A1576 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A1574 " --> pdb=" O LEU A1483 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A1573 " --> pdb=" O ASP A1585 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP A1585 " --> pdb=" O TYR A1573 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY A1575 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ALA A1583 " --> pdb=" O GLY A1575 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER A1577 " --> pdb=" O PRO A1581 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR A1554 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N ASP A1585 " --> pdb=" O THR A1554 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 462 through 464 removed outlier: 6.248A pdb=" N ASN B 462 " --> pdb=" O TRP B 491 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE B 493 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS B 464 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR B 413 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU B 440 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU B 415 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN B 412 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL B 542 " --> pdb=" O GLN B 412 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 414 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 544 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 416 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU B 574 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 541 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE B 576 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B 543 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=10, first strand: chain 'B' and resid 653 through 654 removed outlier: 6.477A pdb=" N VAL B 794 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 833 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 796 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N CYS B 835 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 798 " --> pdb=" O CYS B 835 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ARG B 837 " --> pdb=" O VAL B 798 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS B 731 " --> pdb=" O ILE B 832 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN B 834 " --> pdb=" O LYS B 731 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE B 733 " --> pdb=" O ASN B 834 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET B 836 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU B 735 " --> pdb=" O MET B 836 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL B 853 " --> pdb=" O HIS B 734 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B 736 " --> pdb=" O VAL B 853 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 933 through 934 Processing sheet with id=12, first strand: chain 'B' and resid 1278 through 1280 Processing sheet with id=13, first strand: chain 'B' and resid 1492 through 1494 removed outlier: 3.798A pdb=" N PHE B1481 " --> pdb=" O PHE B1576 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B1574 " --> pdb=" O LEU B1483 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 1492 through 1494 removed outlier: 3.798A pdb=" N PHE B1481 " --> pdb=" O PHE B1576 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B1574 " --> pdb=" O LEU B1483 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR B1573 " --> pdb=" O ASP B1585 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP B1585 " --> pdb=" O TYR B1573 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B1575 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ALA B1583 " --> pdb=" O GLY B1575 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER B1577 " --> pdb=" O PRO B1581 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B1554 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N ASP B1585 " --> pdb=" O THR B1554 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2676 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: 10.41 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18170 1.03 - 1.23: 46 1.23 - 1.42: 7776 1.42 - 1.61: 10680 1.61 - 1.81: 118 Bond restraints: 36790 Sorted by residual: bond pdb=" CB ASP A 930 " pdb=" CG ASP A 930 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.54e-01 bond pdb=" CB ASP B 930 " pdb=" CG ASP B 930 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.54e-01 bond pdb=" CA ASN B1282 " pdb=" CB ASN B1282 " ideal model delta sigma weight residual 1.541 1.532 0.009 1.20e-02 6.94e+03 6.08e-01 bond pdb=" CA ASN A1282 " pdb=" CB ASN A1282 " ideal model delta sigma weight residual 1.541 1.532 0.009 1.20e-02 6.94e+03 6.08e-01 bond pdb=" C4' ATP B1601 " pdb=" O4' ATP B1601 " ideal model delta sigma weight residual 1.444 1.436 0.008 1.10e-02 8.26e+03 4.82e-01 ... (remaining 36785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 64368 1.25 - 2.49: 2086 2.49 - 3.74: 116 3.74 - 4.99: 18 4.99 - 6.23: 8 Bond angle restraints: 66596 Sorted by residual: angle pdb=" N ASN A1282 " pdb=" CA ASN A1282 " pdb=" CB ASN A1282 " ideal model delta sigma weight residual 114.17 110.83 3.34 1.14e+00 7.69e-01 8.58e+00 angle pdb=" N ASN B1282 " pdb=" CA ASN B1282 " pdb=" CB ASN B1282 " ideal model delta sigma weight residual 114.17 110.83 3.34 1.14e+00 7.69e-01 8.58e+00 angle pdb=" C3' ATP B1601 " pdb=" C4' ATP B1601 " pdb=" C5' ATP B1601 " ideal model delta sigma weight residual 115.19 110.34 4.85 1.76e+00 3.23e-01 7.61e+00 angle pdb=" C3' ATP A1601 " pdb=" C4' ATP A1601 " pdb=" C5' ATP A1601 " ideal model delta sigma weight residual 115.19 110.34 4.85 1.76e+00 3.23e-01 7.61e+00 angle pdb=" C2' ATP B1601 " pdb=" C3' ATP B1601 " pdb=" O3' ATP B1601 " ideal model delta sigma weight residual 111.83 105.60 6.23 2.67e+00 1.40e-01 5.46e+00 ... (remaining 66591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15194 17.97 - 35.94: 1444 35.94 - 53.92: 472 53.92 - 71.89: 102 71.89 - 89.86: 28 Dihedral angle restraints: 17240 sinusoidal: 9372 harmonic: 7868 Sorted by residual: dihedral pdb=" CA ASP A1115 " pdb=" CB ASP A1115 " pdb=" CG ASP A1115 " pdb=" OD1 ASP A1115 " ideal model delta sinusoidal sigma weight residual -30.00 -86.33 56.33 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B1115 " pdb=" CB ASP B1115 " pdb=" CG ASP B1115 " pdb=" OD1 ASP B1115 " ideal model delta sinusoidal sigma weight residual -30.00 -86.33 56.33 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CG ARG A 902 " pdb=" CD ARG A 902 " pdb=" NE ARG A 902 " pdb=" CZ ARG A 902 " ideal model delta sinusoidal sigma weight residual -180.00 -135.27 -44.73 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 17237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2434 0.057 - 0.114: 256 0.114 - 0.171: 50 0.171 - 0.228: 0 0.228 - 0.285: 6 Chirality restraints: 2746 Sorted by residual: chirality pdb=" C3' ATP A1601 " pdb=" C2' ATP A1601 " pdb=" C4' ATP A1601 " pdb=" O3' ATP A1601 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' ATP B1601 " pdb=" C2' ATP B1601 " pdb=" C4' ATP B1601 " pdb=" O3' ATP B1601 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C4' ATP A1601 " pdb=" C3' ATP A1601 " pdb=" C5' ATP A1601 " pdb=" O4' ATP A1601 " both_signs ideal model delta sigma weight residual False -2.49 -2.77 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2743 not shown) Planarity restraints: 5258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 554 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A 555 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 555 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 555 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 554 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 555 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 555 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 555 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1430 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A1431 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1431 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1431 " -0.022 5.00e-02 4.00e+02 ... (remaining 5255 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1593 2.18 - 2.78: 71394 2.78 - 3.39: 99717 3.39 - 3.99: 128689 3.99 - 4.60: 203316 Nonbonded interactions: 504709 Sorted by model distance: nonbonded pdb=" OE1 GLN B1375 " pdb=" H THR B1377 " model vdw 1.573 2.450 nonbonded pdb=" OE1 GLN A1375 " pdb=" H THR A1377 " model vdw 1.573 2.450 nonbonded pdb=" HH TYR B 486 " pdb=" O ILE B 533 " model vdw 1.604 2.450 nonbonded pdb=" HH TYR A 486 " pdb=" O ILE A 533 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU B 441 " pdb=" HE1 TRP B 491 " model vdw 1.638 2.450 ... (remaining 504704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 70.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.002 0.024 18574 Z= 0.094 Angle : 0.471 6.234 25036 Z= 0.253 Chirality : 0.039 0.285 2746 Planarity : 0.003 0.043 3150 Dihedral : 17.699 89.861 7042 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.89 % Allowed : 20.42 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 2160 helix: 2.26 (0.16), residues: 1224 sheet: 0.09 (0.35), residues: 206 loop : 0.21 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 459 TYR 0.009 0.001 TYR B1093 PHE 0.011 0.001 PHE B1344 TRP 0.010 0.001 TRP A 586 HIS 0.003 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (18574) covalent geometry : angle 0.47055 / 0.25 (25036) hydrogen bonds : bond 0.13147 / 8.35 ( 916) hydrogen bonds : angle 5.27865 / 3.72 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 GLN cc_start: 0.7259 (mt0) cc_final: 0.6504 (tm-30) REVERT: A 1266 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7872 (ttmm) REVERT: A 1362 MET cc_start: 0.7476 (mmm) cc_final: 0.7156 (mmm) REVERT: A 1381 GLN cc_start: 0.6774 (mm110) cc_final: 0.6529 (mm110) REVERT: B 789 GLN cc_start: 0.7260 (mt0) cc_final: 0.6505 (tm-30) REVERT: B 1266 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7869 (ttmm) REVERT: B 1362 MET cc_start: 0.7473 (mmm) cc_final: 0.7155 (mmm) REVERT: B 1381 GLN cc_start: 0.6774 (mm110) cc_final: 0.6527 (mm110) outliers start: 18 outliers final: 16 residues processed: 154 average time/residue: 0.3112 time to fit residues: 74.2678 Evaluate side-chains 148 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 855 GLN Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 855 GLN Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1361 THR Chi-restraints excluded: chain B residue 1367 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.0770 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN B 449 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102722 restraints weight = 83210.031| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.29 r_work: 0.3193 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18574 Z= 0.214 Angle : 0.493 4.264 25036 Z= 0.268 Chirality : 0.040 0.145 2746 Planarity : 0.004 0.044 3150 Dihedral : 6.974 57.753 2476 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.38 % Allowed : 18.53 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.19), residues: 2160 helix: 2.02 (0.15), residues: 1232 sheet: -0.17 (0.36), residues: 198 loop : -0.03 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.016 0.001 TYR A1093 PHE 0.016 0.001 PHE B 675 TRP 0.008 0.001 TRP A 752 HIS 0.003 0.001 HIS A 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (18574) covalent geometry : angle 0.49253 / 0.27 (25036) hydrogen bonds : bond 0.04437 / 2.91 ( 916) hydrogen bonds : angle 4.29829 / 3.01 ( 2676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7259 (mt0) REVERT: A 751 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8893 (mp) REVERT: A 789 GLN cc_start: 0.7338 (mt0) cc_final: 0.6510 (tm-30) REVERT: A 1088 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 1157 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: A 1266 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8125 (mtpp) REVERT: A 1362 MET cc_start: 0.7628 (mmm) cc_final: 0.7243 (mmm) REVERT: A 1381 GLN cc_start: 0.6823 (mm110) cc_final: 0.6487 (mm110) REVERT: B 424 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: B 751 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8891 (mp) REVERT: B 789 GLN cc_start: 0.7339 (mt0) cc_final: 0.6523 (tm-30) REVERT: B 1088 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8721 (tt) REVERT: B 1157 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: B 1266 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8129 (mtpp) REVERT: B 1362 MET cc_start: 0.7623 (mmm) cc_final: 0.7239 (mmm) REVERT: B 1381 GLN cc_start: 0.6821 (mm110) cc_final: 0.6484 (mm110) outliers start: 48 outliers final: 26 residues processed: 184 average time/residue: 0.2985 time to fit residues: 86.1161 Evaluate side-chains 168 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1471 MET Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1157 GLU Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1360 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1380 ILE Chi-restraints excluded: chain B residue 1396 SER Chi-restraints excluded: chain B residue 1471 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [95, 114, 147, 88, 80, 107, 25, 137, 171, 67, 70] chunk 95 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104847 restraints weight = 82847.594| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.29 r_work: 0.3222 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18574 Z= 0.109 Angle : 0.433 4.212 25036 Z= 0.231 Chirality : 0.038 0.136 2746 Planarity : 0.003 0.044 3150 Dihedral : 6.528 56.879 2464 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.49 % Allowed : 18.93 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 2160 helix: 2.38 (0.15), residues: 1208 sheet: -0.24 (0.36), residues: 198 loop : 0.13 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.014 0.001 TYR A1093 PHE 0.011 0.001 PHE B 675 TRP 0.006 0.001 TRP B 586 HIS 0.002 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (18574) covalent geometry : angle 0.43328 / 0.23 (25036) hydrogen bonds : bond 0.03577 / 2.35 ( 916) hydrogen bonds : angle 3.97907 / 2.80 ( 2676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.9110 (t) cc_final: 0.8628 (m) REVERT: A 789 GLN cc_start: 0.7289 (mt0) cc_final: 0.6492 (tm-30) REVERT: A 1088 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 1266 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7969 (ttmm) REVERT: A 1362 MET cc_start: 0.7615 (mmm) cc_final: 0.7230 (mmm) REVERT: B 481 SER cc_start: 0.9116 (t) cc_final: 0.8635 (m) REVERT: B 789 GLN cc_start: 0.7284 (mt0) cc_final: 0.6490 (tm-30) REVERT: B 1088 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 1266 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7965 (ttmm) REVERT: B 1362 MET cc_start: 0.7609 (mmm) cc_final: 0.7225 (mmm) outliers start: 30 outliers final: 20 residues processed: 164 average time/residue: 0.3009 time to fit residues: 77.4101 Evaluate side-chains 156 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1396 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [21, 132, 48, 153, 9, 113, 107, 189, 78, 92, 198] chunk 21 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 198 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105001 restraints weight = 82408.740| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.29 r_work: 0.3226 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18574 Z= 0.107 Angle : 0.422 4.291 25036 Z= 0.224 Chirality : 0.038 0.133 2746 Planarity : 0.003 0.043 3150 Dihedral : 6.380 56.178 2460 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.98 % Allowed : 17.94 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.19), residues: 2160 helix: 2.46 (0.15), residues: 1208 sheet: -0.31 (0.37), residues: 194 loop : 0.16 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 459 TYR 0.013 0.001 TYR A1093 PHE 0.010 0.001 PHE B 675 TRP 0.006 0.001 TRP B 586 HIS 0.003 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (18574) covalent geometry : angle 0.42157 / 0.22 (25036) hydrogen bonds : bond 0.03293 / 2.17 ( 916) hydrogen bonds : angle 3.85057 / 2.71 ( 2676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 SER cc_start: 0.9087 (t) cc_final: 0.8611 (m) REVERT: A 789 GLN cc_start: 0.7293 (mt0) cc_final: 0.6455 (tm-30) REVERT: A 1088 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8710 (tt) REVERT: A 1266 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7924 (ttmm) REVERT: A 1362 MET cc_start: 0.7642 (mmm) cc_final: 0.7316 (mmm) REVERT: B 481 SER cc_start: 0.9086 (t) cc_final: 0.8610 (m) REVERT: B 789 GLN cc_start: 0.7291 (mt0) cc_final: 0.6454 (tm-30) REVERT: B 1088 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8707 (tt) REVERT: B 1266 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7922 (ttmm) REVERT: B 1362 MET cc_start: 0.7633 (mmm) cc_final: 0.7310 (mmm) outliers start: 40 outliers final: 28 residues processed: 180 average time/residue: 0.3041 time to fit residues: 86.1285 Evaluate side-chains 166 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1550 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [147, 200, 195, 82, 117, 94, 145, 55, 12, 51, 36] chunk 147 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104252 restraints weight = 82637.833| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.27 r_work: 0.3215 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18574 Z= 0.145 Angle : 0.438 4.357 25036 Z= 0.234 Chirality : 0.038 0.132 2746 Planarity : 0.003 0.043 3150 Dihedral : 6.470 56.296 2460 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.98 % Allowed : 18.43 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.19), residues: 2160 helix: 2.39 (0.15), residues: 1208 sheet: -0.43 (0.37), residues: 194 loop : 0.06 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.015 0.001 TYR B1093 PHE 0.014 0.001 PHE B 675 TRP 0.006 0.001 TRP A 586 HIS 0.002 0.001 HIS A 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (18574) covalent geometry : angle 0.43848 / 0.23 (25036) hydrogen bonds : bond 0.03539 / 2.34 ( 916) hydrogen bonds : angle 3.85115 / 2.71 ( 2676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7195 (mt0) REVERT: A 481 SER cc_start: 0.9084 (t) cc_final: 0.8611 (m) REVERT: A 751 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8909 (mp) REVERT: A 1088 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8776 (tt) REVERT: A 1266 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8047 (ttmm) REVERT: A 1362 MET cc_start: 0.7662 (mmm) cc_final: 0.7320 (mmm) REVERT: B 424 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7179 (mt0) REVERT: B 481 SER cc_start: 0.9089 (t) cc_final: 0.8618 (m) REVERT: B 751 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8905 (mp) REVERT: B 1088 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8774 (tt) REVERT: B 1266 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8036 (ttmm) REVERT: B 1362 MET cc_start: 0.7660 (mmm) cc_final: 0.7318 (mmm) outliers start: 40 outliers final: 26 residues processed: 180 average time/residue: 0.2983 time to fit residues: 84.8060 Evaluate side-chains 172 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1396 SER Chi-restraints excluded: chain B residue 1550 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [165, 153, 121, 145, 94, 17, 87, 125, 128, 126, 92] chunk 165 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104892 restraints weight = 82717.261| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.29 r_work: 0.3223 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18574 Z= 0.109 Angle : 0.422 4.253 25036 Z= 0.224 Chirality : 0.038 0.134 2746 Planarity : 0.003 0.042 3150 Dihedral : 6.321 55.709 2456 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.98 % Allowed : 18.24 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.19), residues: 2160 helix: 2.48 (0.15), residues: 1208 sheet: -0.44 (0.37), residues: 194 loop : 0.13 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.014 0.001 TYR B1093 PHE 0.011 0.001 PHE B 675 TRP 0.006 0.001 TRP B 586 HIS 0.002 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (18574) covalent geometry : angle 0.42182 / 0.22 (25036) hydrogen bonds : bond 0.03254 / 2.15 ( 916) hydrogen bonds : angle 3.76382 / 2.65 ( 2676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7086 (mt0) REVERT: A 481 SER cc_start: 0.9070 (t) cc_final: 0.8604 (m) REVERT: A 1088 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8762 (tt) REVERT: A 1266 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8044 (ttmm) REVERT: A 1362 MET cc_start: 0.7663 (mmm) cc_final: 0.7309 (mmm) REVERT: B 424 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7075 (mt0) REVERT: B 481 SER cc_start: 0.9074 (t) cc_final: 0.8607 (m) REVERT: B 1088 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8758 (tt) REVERT: B 1266 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8036 (ttmm) REVERT: B 1362 MET cc_start: 0.7655 (mmm) cc_final: 0.7304 (mmm) outliers start: 40 outliers final: 32 residues processed: 176 average time/residue: 0.2997 time to fit residues: 83.3272 Evaluate side-chains 174 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1345 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1396 SER Chi-restraints excluded: chain B residue 1550 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [96, 178, 25, 194, 186, 98, 50, 43, 45, 11, 207] chunk 96 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104113 restraints weight = 82771.505| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.29 r_work: 0.3213 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18574 Z= 0.137 Angle : 0.431 4.375 25036 Z= 0.230 Chirality : 0.038 0.132 2746 Planarity : 0.003 0.042 3150 Dihedral : 6.372 55.386 2456 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 18.04 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.19), residues: 2160 helix: 2.43 (0.15), residues: 1208 sheet: -0.50 (0.37), residues: 194 loop : 0.06 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.014 0.001 TYR A1093 PHE 0.013 0.001 PHE A 675 TRP 0.006 0.001 TRP B 586 HIS 0.002 0.001 HIS B1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (18574) covalent geometry : angle 0.43134 / 0.23 (25036) hydrogen bonds : bond 0.03424 / 2.26 ( 916) hydrogen bonds : angle 3.77075 / 2.66 ( 2676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7156 (mt0) REVERT: A 481 SER cc_start: 0.9073 (t) cc_final: 0.8602 (m) REVERT: A 751 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 1088 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8799 (tt) REVERT: A 1266 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8044 (ttmm) REVERT: A 1362 MET cc_start: 0.7701 (mmm) cc_final: 0.7377 (mmm) REVERT: B 424 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: B 481 SER cc_start: 0.9078 (t) cc_final: 0.8608 (m) REVERT: B 751 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8891 (mp) REVERT: B 1088 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8795 (tt) REVERT: B 1266 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (ttmm) REVERT: B 1362 MET cc_start: 0.7696 (mmm) cc_final: 0.7370 (mmm) outliers start: 44 outliers final: 34 residues processed: 182 average time/residue: 0.2959 time to fit residues: 85.2272 Evaluate side-chains 178 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1345 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1380 ILE Chi-restraints excluded: chain B residue 1396 SER Chi-restraints excluded: chain B residue 1550 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [18, 143, 96, 54, 13, 135, 184, 146, 179, 108, 98] chunk 18 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 146 optimal weight: 0.0770 chunk 179 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1252 ASN B1252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105649 restraints weight = 82349.559| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.27 r_work: 0.3240 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18574 Z= 0.087 Angle : 0.414 4.370 25036 Z= 0.218 Chirality : 0.037 0.134 2746 Planarity : 0.003 0.042 3150 Dihedral : 6.192 54.532 2456 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.98 % Allowed : 18.24 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 2160 helix: 2.59 (0.15), residues: 1210 sheet: -0.44 (0.37), residues: 194 loop : 0.18 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.013 0.001 TYR B1093 PHE 0.009 0.001 PHE A 675 TRP 0.006 0.001 TRP A 586 HIS 0.003 0.000 HIS B1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (18574) covalent geometry : angle 0.41386 / 0.22 (25036) hydrogen bonds : bond 0.02986 / 1.97 ( 916) hydrogen bonds : angle 3.67076 / 2.59 ( 2676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7010 (mt0) REVERT: A 449 ASN cc_start: 0.7912 (t0) cc_final: 0.7577 (p0) REVERT: A 481 SER cc_start: 0.9077 (t) cc_final: 0.8603 (m) REVERT: A 1088 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8767 (tt) REVERT: A 1266 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8035 (ttmm) REVERT: A 1362 MET cc_start: 0.7630 (mmm) cc_final: 0.7300 (mmm) REVERT: B 424 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7008 (mt0) REVERT: B 449 ASN cc_start: 0.7907 (t0) cc_final: 0.7569 (p0) REVERT: B 481 SER cc_start: 0.9076 (t) cc_final: 0.8605 (m) REVERT: B 1088 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8758 (tt) REVERT: B 1266 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8023 (ttmm) REVERT: B 1362 MET cc_start: 0.7625 (mmm) cc_final: 0.7297 (mmm) outliers start: 40 outliers final: 34 residues processed: 178 average time/residue: 0.2914 time to fit residues: 82.1225 Evaluate side-chains 174 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1266 LYS Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1266 LYS Chi-restraints excluded: chain B residue 1345 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1396 SER Chi-restraints excluded: chain B residue 1467 GLN Chi-restraints excluded: chain B residue 1550 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [136, 135, 39, 72, 86, 200, 2, 207, 215, 46, 170] chunk 136 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.142016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105580 restraints weight = 82824.777| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.28 r_work: 0.3238 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18574 Z= 0.095 Angle : 0.410 4.399 25036 Z= 0.216 Chirality : 0.038 0.131 2746 Planarity : 0.003 0.043 3150 Dihedral : 6.150 53.750 2456 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.78 % Allowed : 18.33 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.19), residues: 2160 helix: 2.62 (0.15), residues: 1208 sheet: -0.45 (0.37), residues: 194 loop : 0.22 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 536 TYR 0.013 0.001 TYR A1093 PHE 0.010 0.001 PHE A 675 TRP 0.006 0.001 TRP B 586 HIS 0.002 0.001 HIS B1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (18574) covalent geometry : angle 0.41016 / 0.22 (25036) hydrogen bonds : bond 0.02974 / 1.96 ( 916) hydrogen bonds : angle 3.64570 / 2.58 ( 2676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7033 (mt0) REVERT: A 481 SER cc_start: 0.9086 (t) cc_final: 0.8606 (m) REVERT: A 1088 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8776 (tt) REVERT: A 1362 MET cc_start: 0.7633 (mmm) cc_final: 0.7301 (mmm) REVERT: A 1381 GLN cc_start: 0.6876 (mm110) cc_final: 0.6645 (mm110) REVERT: B 424 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7035 (mt0) REVERT: B 481 SER cc_start: 0.9085 (t) cc_final: 0.8607 (m) REVERT: B 1088 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8769 (tt) REVERT: B 1362 MET cc_start: 0.7631 (mmm) cc_final: 0.7304 (mmm) REVERT: B 1381 GLN cc_start: 0.6874 (mm110) cc_final: 0.6646 (mm110) outliers start: 36 outliers final: 32 residues processed: 170 average time/residue: 0.2903 time to fit residues: 78.7967 Evaluate side-chains 170 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1345 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1467 GLN Chi-restraints excluded: chain B residue 1550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [60, 206, 126, 161, 107, 152, 16, 20, 37, 163, 13] chunk 60 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 152 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 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 = 0.3809 r_free = 0.3809 target = 0.141133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104688 restraints weight = 83256.573| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.29 r_work: 0.3226 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18574 Z= 0.128 Angle : 0.427 4.455 25036 Z= 0.228 Chirality : 0.038 0.132 2746 Planarity : 0.003 0.042 3150 Dihedral : 6.087 53.550 2448 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.98 % Allowed : 18.24 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 2160 helix: 2.55 (0.15), residues: 1208 sheet: -0.51 (0.37), residues: 194 loop : 0.16 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 536 TYR 0.014 0.001 TYR B1093 PHE 0.012 0.001 PHE B 675 TRP 0.006 0.001 TRP B 586 HIS 0.002 0.001 HIS B1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (18574) covalent geometry : angle 0.42680 / 0.23 (25036) hydrogen bonds : bond 0.03198 / 2.11 ( 916) hydrogen bonds : angle 3.69605 / 2.64 ( 2676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 744 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: A 481 SER cc_start: 0.9079 (t) cc_final: 0.8603 (m) REVERT: A 1088 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8818 (tt) REVERT: A 1362 MET cc_start: 0.7633 (mmm) cc_final: 0.7297 (mmm) REVERT: A 1381 GLN cc_start: 0.6920 (mm110) cc_final: 0.6692 (mm110) REVERT: B 424 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7223 (mt0) REVERT: B 481 SER cc_start: 0.9077 (t) cc_final: 0.8602 (m) REVERT: B 1088 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8812 (tt) REVERT: B 1362 MET cc_start: 0.7627 (mmm) cc_final: 0.7297 (mmm) REVERT: B 1381 GLN cc_start: 0.6913 (mm110) cc_final: 0.6695 (mm110) outliers start: 40 outliers final: 36 residues processed: 174 average time/residue: 0.2910 time to fit residues: 80.6278 Evaluate side-chains 178 residues out of total 2018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1093 TYR Chi-restraints excluded: chain A residue 1143 ASN Chi-restraints excluded: chain A residue 1208 ILE Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1550 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 646 GLU Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain B residue 1237 ASP Chi-restraints excluded: chain B residue 1345 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1380 ILE Chi-restraints excluded: chain B residue 1396 SER Chi-restraints excluded: chain B residue 1467 GLN Chi-restraints excluded: chain B residue 1550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [145, 24, 146, 61, 26, 68, 123, 202, 58, 169, 136] chunk 145 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 202 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 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 = 0.3809 r_free = 0.3809 target = 0.141126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104694 restraints weight = 82515.853| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.28 r_work: 0.3227 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18574 Z= 0.125 Angle : 0.435 6.429 25036 Z= 0.233 Chirality : 0.038 0.133 2746 Planarity : 0.003 0.042 3150 Dihedral : 6.082 53.034 2448 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.08 % Allowed : 18.33 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 2160 helix: 2.54 (0.15), residues: 1208 sheet: -0.52 (0.37), residues: 194 loop : 0.16 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.014 0.001 TYR A1093 PHE 0.012 0.001 PHE A 675 TRP 0.006 0.001 TRP B 586 HIS 0.002 0.001 HIS A1091 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (18574) covalent geometry : angle 0.43482 / 0.23 (25036) hydrogen bonds : bond 0.03175 / 2.09 ( 916) hydrogen bonds : angle 3.71708 / 2.69 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10157.11 seconds wall clock time: 172 minutes 26.03 seconds (10346.03 seconds total)