Starting phenix.real_space_refine on Thu Mar 5 04:31:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zjw_74344/03_2026/9zjw_74344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zjw_74344/03_2026/9zjw_74344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zjw_74344/03_2026/9zjw_74344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zjw_74344/03_2026/9zjw_74344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zjw_74344/03_2026/9zjw_74344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zjw_74344/03_2026/9zjw_74344.map" } resolution = 2.8 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 80 5.16 5 C 11840 2.51 5 N 3034 2.21 5 O 3402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18364 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 9150 Classifications: {'peptide': 1117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1077} Chain breaks: 11 Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 9150 Classifications: {'peptide': 1117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1077} Chain breaks: 11 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} Chain: "B" 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} Time building chain proxies: 4.20, per 1000 atoms: 0.23 Number of scatterers: 18364 At special positions: 0 Unit cell: (125.4, 115.5, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 6 15.00 Mg 2 11.99 O 3402 8.00 N 3034 7.00 C 11840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 692.9 milliseconds 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 12 sheets defined 62.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 389 through 400 removed outlier: 4.152A pdb=" N LYS A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.876A pdb=" N LYS A 426 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.921A pdb=" N ILE A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) 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 470 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 Processing helix chain 'A' and resid 554 through 568 removed outlier: 3.567A 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 620 removed outlier: 3.678A pdb=" N LYS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 664 through 667 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.636A pdb=" N GLY A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.814A pdb=" N PHE A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 805 through 821 Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 858 through 876 removed outlier: 3.911A pdb=" N GLU A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) removed outlier: 3.993A 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: 3.539A 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 943 Processing helix chain 'A' and resid 956 through 961 Processing helix chain 'A' and resid 962 through 965 removed outlier: 3.779A 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 1001 Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1023 through 1036 Processing helix chain 'A' and resid 1052 through 1062 Processing helix chain 'A' and resid 1064 through 1078 Processing helix chain 'A' and resid 1081 through 1095 removed outlier: 3.919A pdb=" N CYS A1085 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1113 Processing helix chain 'A' and resid 1116 through 1139 removed outlier: 3.639A pdb=" N SER A1120 " --> pdb=" O ASN A1116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A1130 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1174 removed outlier: 3.915A pdb=" N GLU A1174 " --> pdb=" O SER A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1212 removed outlier: 3.599A pdb=" N GLN A1198 " --> pdb=" O ILE A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 6.175A pdb=" N PHE A1216 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A1218 " --> pdb=" O PRO A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1244 through 1252 removed outlier: 4.069A 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 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1285 through 1308 removed outlier: 4.201A pdb=" N GLU A1289 " --> pdb=" O LYS A1285 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A1290 " --> pdb=" O GLN A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1339 Processing helix chain 'A' and resid 1343 through 1350 removed outlier: 3.882A pdb=" N TYR A1350 " --> pdb=" O GLY A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1353 No H-bonds generated for 'chain 'A' and resid 1351 through 1353' Processing helix chain 'A' and resid 1354 through 1375 Processing helix chain 'A' and resid 1381 through 1399 removed outlier: 3.613A pdb=" N LYS A1385 " --> pdb=" O GLN A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1423 removed outlier: 4.016A pdb=" N LEU A1411 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Proline residue: A1421 - end of helix Processing helix chain 'A' and resid 1429 through 1440 removed outlier: 4.018A pdb=" N TRP A1440 " --> pdb=" O SER A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1451 removed outlier: 3.634A pdb=" N GLU A1451 " --> pdb=" O GLN A1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1448 through 1451' Processing helix chain 'A' and resid 1452 through 1468 Processing helix chain 'A' and resid 1487 through 1490 Processing helix chain 'A' and resid 1495 through 1502 removed outlier: 3.791A pdb=" N PHE A1502 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1525 Processing helix chain 'A' and resid 1557 through 1561 removed outlier: 3.547A pdb=" N GLN A1560 " --> pdb=" O PHE A1557 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.876A pdb=" N LYS B 426 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.927A pdb=" N ILE B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 450 through 457 Processing helix chain 'B' and resid 465 through 470 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: 3.522A pdb=" N VAL B 521 " --> pdb=" O ARG B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 removed outlier: 3.530A pdb=" N GLU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.512A pdb=" N LEU B 589 " --> pdb=" O GLY B 585 " (cutoff:3.500A) 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 620 removed outlier: 3.547A pdb=" N LYS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 649 removed outlier: 3.537A pdb=" N ILE B 648 " --> pdb=" O LYS B 644 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 667 removed outlier: 3.521A pdb=" N LYS B 667 " --> pdb=" O LEU B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 667' Processing helix chain 'B' and resid 668 through 686 Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.852A pdb=" N PHE B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.526A pdb=" N GLY B 774 " --> pdb=" O PHE B 770 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 4.410A pdb=" N VAL B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 4.225A 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: 3.928A pdb=" N GLU B 874 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.714A 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 removed outlier: 3.521A pdb=" N MET B 888 " --> pdb=" O SER B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 906 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 removed outlier: 3.581A pdb=" N GLY B 961 " --> pdb=" O GLU B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 removed outlier: 3.682A 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 1001 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1023 through 1036 Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1063 through 1078 removed outlier: 3.869A pdb=" N VAL B1067 " --> pdb=" O GLY B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1095 removed outlier: 3.948A pdb=" N CYS B1085 " --> pdb=" O ASN B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1113 Processing helix chain 'B' and resid 1116 through 1139 removed outlier: 3.665A pdb=" N LYS B1130 " --> pdb=" O VAL B1126 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B1131 " --> pdb=" O TYR B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1142 No H-bonds generated for 'chain 'B' and resid 1140 through 1142' Processing helix chain 'B' and resid 1145 through 1174 removed outlier: 3.617A pdb=" N ALA B1151 " --> pdb=" O ASP B1147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B1174 " --> pdb=" O SER B1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1212 Processing helix chain 'B' and resid 1213 through 1218 removed outlier: 6.125A pdb=" N PHE B1216 " --> pdb=" O LEU B1213 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B1218 " --> pdb=" O PRO B1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1233 Processing helix chain 'B' and resid 1244 through 1253 removed outlier: 4.186A pdb=" N ASN B1252 " --> pdb=" O LEU B1248 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR B1253 " --> pdb=" O ALA B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1253 through 1258 Processing helix chain 'B' and resid 1259 through 1276 Processing helix chain 'B' and resid 1282 through 1284 No H-bonds generated for 'chain 'B' and resid 1282 through 1284' Processing helix chain 'B' and resid 1285 through 1308 removed outlier: 4.062A 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 1353 Processing helix chain 'B' and resid 1354 through 1375 removed outlier: 4.367A pdb=" N CYS B1364 " --> pdb=" O SER B1360 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1399 removed outlier: 3.539A pdb=" N LEU B1390 " --> pdb=" O LEU B1386 " (cutoff:3.500A) Processing helix chain 'B' and resid 1407 through 1420 Processing helix chain 'B' and resid 1429 through 1440 removed outlier: 3.583A pdb=" N LEU B1434 " --> pdb=" O GLU B1430 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP B1440 " --> pdb=" O SER B1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 1448 through 1451 removed outlier: 4.061A pdb=" N GLU B1451 " --> pdb=" O GLN B1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1448 through 1451' Processing helix chain 'B' and resid 1452 through 1468 Processing helix chain 'B' and resid 1469 through 1472 removed outlier: 3.696A pdb=" N HIS B1472 " --> pdb=" O LYS B1469 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1469 through 1472' 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 Processing helix chain 'B' and resid 1557 through 1561 removed outlier: 3.737A pdb=" N GLN B1560 " --> pdb=" O PHE B1557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 7.129A pdb=" N TYR A 413 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LEU A 440 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 415 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN A 412 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL A 542 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 414 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU A 544 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 416 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU A 574 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 541 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A 576 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE A 543 " --> pdb=" O ILE A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 631 through 632 Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 655 removed outlier: 4.271A pdb=" N CYS A 760 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP A 799 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 794 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 833 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 796 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N CYS A 835 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 798 " --> pdb=" O CYS A 835 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ALA A 837 " --> pdb=" O VAL A 798 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS A 731 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASN A 834 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 733 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET A 836 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU A 735 " --> pdb=" O MET A 836 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 933 through 934 removed outlier: 3.568A pdb=" N TYR A 978 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1278 through 1280 Processing sheet with id=AA6, first strand: chain 'A' and resid 1492 through 1494 removed outlier: 3.531A pdb=" N PHE A1481 " --> pdb=" O PHE A1576 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU A1574 " --> pdb=" O LEU A1483 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A1573 " --> pdb=" O ASP A1585 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASP A1585 " --> pdb=" O TYR A1573 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A1575 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA A1583 " --> pdb=" O GLY A1575 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A1577 " --> pdb=" O PRO A1581 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ALA A1583 " --> pdb=" O PRO A1552 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR A1554 " --> pdb=" O ALA A1583 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ASP A1585 " --> pdb=" O THR A1554 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A1541 " --> pdb=" O ILE A1551 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLU A1542 " --> pdb=" O GLN A1531 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLN A1531 " --> pdb=" O GLU A1542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 462 through 464 removed outlier: 6.105A pdb=" N ASN B 462 " --> pdb=" O TRP B 491 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE B 493 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS B 464 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 490 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR B 413 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LEU B 440 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 415 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 412 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL B 542 " --> pdb=" O GLN B 412 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 414 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 544 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 416 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE B 606 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS B 575 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=AA9, first strand: chain 'B' and resid 652 through 654 removed outlier: 5.343A pdb=" N ASP B 799 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 794 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU B 833 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 796 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N CYS B 835 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 798 " --> pdb=" O CYS B 835 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ALA B 837 " --> pdb=" O VAL B 798 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS B 731 " --> pdb=" O ILE B 832 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN B 834 " --> pdb=" O LYS B 731 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 733 " --> pdb=" O ASN B 834 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N MET B 836 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 735 " --> pdb=" O MET B 836 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 933 through 934 removed outlier: 3.537A pdb=" N TYR B 978 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1278 through 1280 Processing sheet with id=AB3, first strand: chain 'B' and resid 1492 through 1494 removed outlier: 3.563A pdb=" N PHE B1481 " --> pdb=" O PHE B1576 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU B1574 " --> pdb=" O LEU B1483 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B1573 " --> pdb=" O ASP B1585 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP B1585 " --> pdb=" O TYR B1573 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY B1575 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA B1583 " --> pdb=" O GLY B1575 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA B1583 " --> pdb=" O PRO B1552 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B1554 " --> pdb=" O ALA B1583 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N ASP B1585 " --> pdb=" O THR B1554 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU B1542 " --> pdb=" O GLN B1531 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLN B1531 " --> pdb=" O GLU B1542 " (cutoff:3.500A) 954 hydrogen bonds defined for protein. 2757 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: 3.18 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5803 1.34 - 1.46: 4168 1.46 - 1.58: 8661 1.58 - 1.70: 4 1.70 - 1.82: 116 Bond restraints: 18752 Sorted by residual: bond pdb=" CB MET A1453 " pdb=" CG MET A1453 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CB ASP B1190 " pdb=" CG ASP B1190 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.84e+00 bond pdb=" SD MET A1453 " pdb=" CE MET A1453 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.68e+00 bond pdb=" CB ARG A1403 " pdb=" CG ARG A1403 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CB LYS A1301 " pdb=" CG LYS A1301 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 18747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 25021 2.41 - 4.82: 224 4.82 - 7.23: 27 7.23 - 9.63: 6 9.63 - 12.04: 4 Bond angle restraints: 25282 Sorted by residual: angle pdb=" CB LYS A1301 " pdb=" CG LYS A1301 " pdb=" CD LYS A1301 " ideal model delta sigma weight residual 111.30 120.92 -9.62 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CB ARG A1403 " pdb=" CG ARG A1403 " pdb=" CD ARG A1403 " ideal model delta sigma weight residual 111.30 120.74 -9.44 2.30e+00 1.89e-01 1.68e+01 angle pdb=" CB MET A 786 " pdb=" CG MET A 786 " pdb=" SD MET A 786 " ideal model delta sigma weight residual 112.70 124.74 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C TYR B1253 " pdb=" N ILE B1254 " pdb=" CA ILE B1254 " ideal model delta sigma weight residual 120.33 123.39 -3.06 8.00e-01 1.56e+00 1.47e+01 angle pdb=" CB MET A1362 " pdb=" CG MET A1362 " pdb=" SD MET A1362 " ideal model delta sigma weight residual 112.70 123.08 -10.38 3.00e+00 1.11e-01 1.20e+01 ... (remaining 25277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9687 17.92 - 35.83: 1242 35.83 - 53.75: 345 53.75 - 71.67: 84 71.67 - 89.58: 24 Dihedral angle restraints: 11382 sinusoidal: 4800 harmonic: 6582 Sorted by residual: dihedral pdb=" CA PRO A1407 " pdb=" C PRO A1407 " pdb=" N VAL A1408 " pdb=" CA VAL A1408 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLN A1381 " pdb=" C GLN A1381 " pdb=" N SER A1382 " pdb=" CA SER A1382 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA MET B 534 " pdb=" C MET B 534 " pdb=" N PRO B 535 " pdb=" CA PRO B 535 " ideal model delta harmonic sigma weight residual -180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 11379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1913 0.037 - 0.074: 629 0.074 - 0.110: 193 0.110 - 0.147: 31 0.147 - 0.184: 6 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CG LEU A1351 " pdb=" CB LEU A1351 " pdb=" CD1 LEU A1351 " pdb=" CD2 LEU A1351 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CB ILE B1365 " pdb=" CA ILE B1365 " pdb=" CG1 ILE B1365 " pdb=" CG2 ILE B1365 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA ASN B 787 " pdb=" N ASN B 787 " pdb=" C ASN B 787 " pdb=" CB ASN B 787 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 2769 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B1300 " -0.009 2.00e-02 2.50e+03 1.18e-02 2.43e+00 pdb=" CG PHE B1300 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B1300 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B1300 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B1300 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B1300 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B1300 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1488 " -0.118 9.50e-02 1.11e+02 5.36e-02 2.40e+00 pdb=" NE ARG A1488 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A1488 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A1488 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A1488 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1399 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A1400 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A1400 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1400 " 0.021 5.00e-02 4.00e+02 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 136 2.55 - 3.14: 13859 3.14 - 3.73: 28212 3.73 - 4.31: 39599 4.31 - 4.90: 66687 Nonbonded interactions: 148493 Sorted by model distance: nonbonded pdb=" O2G ATP B1601 " pdb="MG MG B1602 " model vdw 1.965 2.170 nonbonded pdb=" O2B ATP A1601 " pdb="MG MG A1602 " model vdw 2.009 2.170 nonbonded pdb=" O2G ATP A1601 " pdb="MG MG A1602 " model vdw 2.062 2.170 nonbonded pdb=" OG1 THR A 744 " pdb="MG MG A1602 " model vdw 2.079 2.170 nonbonded pdb=" OH TYR B 486 " pdb=" O ILE B 533 " model vdw 2.084 3.040 ... (remaining 148488 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: 8.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.710 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 : 0.003 0.043 18752 Z= 0.152 Angle : 0.582 12.043 25282 Z= 0.313 Chirality : 0.041 0.184 2772 Planarity : 0.004 0.054 3188 Dihedral : 17.562 89.585 7110 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.42 % Allowed : 23.97 % Favored : 74.61 % 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: 1.61 (0.18), residues: 2186 helix: 1.75 (0.15), residues: 1214 sheet: 0.93 (0.37), residues: 204 loop : 0.12 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1488 TYR 0.025 0.001 TYR B1227 PHE 0.027 0.001 PHE B1300 TRP 0.009 0.001 TRP A 586 HIS 0.002 0.001 HIS B1032 Details of bonding type rmsd covalent geometry : bond 0.00343 (18752) covalent geometry : angle 0.58157 (25282) hydrogen bonds : bond 0.20849 ( 954) hydrogen bonds : angle 6.41983 ( 2757) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 0.818 Fit side-chains REVERT: A 396 LYS cc_start: 0.7173 (mtpp) cc_final: 0.6812 (ttpt) REVERT: A 449 ASN cc_start: 0.8052 (t0) cc_final: 0.7150 (p0) REVERT: A 506 LYS cc_start: 0.7555 (pttt) cc_final: 0.7095 (mptt) REVERT: A 509 ASP cc_start: 0.6668 (p0) cc_final: 0.5607 (p0) REVERT: A 570 MET cc_start: 0.8235 (ptm) cc_final: 0.7794 (ttp) REVERT: A 622 LYS cc_start: 0.8375 (pttt) cc_final: 0.8117 (pttt) REVERT: A 681 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7560 (tt0) REVERT: A 703 SER cc_start: 0.8749 (m) cc_final: 0.8506 (t) REVERT: A 728 THR cc_start: 0.6140 (m) cc_final: 0.5638 (t) REVERT: A 786 MET cc_start: 0.7454 (mmm) cc_final: 0.6354 (mpp) REVERT: A 788 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7645 (ttm110) REVERT: A 820 LYS cc_start: 0.6263 (ttmm) cc_final: 0.5963 (mptt) REVERT: A 843 LYS cc_start: 0.7281 (ttmm) cc_final: 0.6759 (ttmt) REVERT: A 860 LYS cc_start: 0.6879 (ptpp) cc_final: 0.6609 (ptpt) REVERT: A 910 ILE cc_start: 0.8273 (pt) cc_final: 0.8023 (mp) REVERT: A 994 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6876 (mt-10) REVERT: A 997 LYS cc_start: 0.6924 (tttt) cc_final: 0.6454 (tptp) REVERT: A 1073 GLU cc_start: 0.7405 (tp30) cc_final: 0.7117 (mm-30) REVERT: A 1200 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7291 (tt0) REVERT: A 1284 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5377 (tt) REVERT: A 1291 LYS cc_start: 0.7401 (mtmm) cc_final: 0.7176 (mttt) REVERT: A 1342 ASP cc_start: 0.7518 (t0) cc_final: 0.6838 (p0) REVERT: A 1453 MET cc_start: 0.5605 (mmt) cc_final: 0.4201 (mpp) REVERT: A 1465 LYS cc_start: 0.7887 (tttm) cc_final: 0.7303 (tppt) REVERT: A 1524 GLN cc_start: 0.7325 (mt0) cc_final: 0.7052 (mp10) REVERT: A 1554 THR cc_start: 0.7231 (m) cc_final: 0.6907 (p) REVERT: B 478 GLU cc_start: 0.5970 (pm20) cc_final: 0.5717 (tp30) REVERT: B 509 ASP cc_start: 0.5457 (p0) cc_final: 0.4879 (p0) REVERT: B 553 ARG cc_start: 0.5300 (mtp-110) cc_final: 0.4747 (mtm-85) REVERT: B 712 GLU cc_start: 0.7157 (pm20) cc_final: 0.6785 (tm-30) REVERT: B 713 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6929 (ttp80) REVERT: B 802 GLU cc_start: 0.6851 (mp0) cc_final: 0.6545 (mp0) REVERT: B 803 GLU cc_start: 0.6510 (mt-10) cc_final: 0.5790 (mt-10) REVERT: B 804 GLN cc_start: 0.7434 (mp10) cc_final: 0.6575 (mm-40) REVERT: B 820 LYS cc_start: 0.7191 (ttmm) cc_final: 0.6914 (mtpt) REVERT: B 824 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.6947 (mmp-170) REVERT: B 903 ASN cc_start: 0.7651 (m-40) cc_final: 0.7157 (t0) REVERT: B 914 GLU cc_start: 0.7703 (mp0) cc_final: 0.7495 (mp0) REVERT: B 955 LYS cc_start: 0.6346 (ttmm) cc_final: 0.5846 (tptt) REVERT: B 958 ASP cc_start: 0.8190 (m-30) cc_final: 0.7931 (m-30) REVERT: B 1111 ILE cc_start: 0.7559 (mt) cc_final: 0.7233 (pt) REVERT: B 1269 ASP cc_start: 0.5887 (m-30) cc_final: 0.5667 (p0) REVERT: B 1362 MET cc_start: 0.3099 (tpt) cc_final: 0.2648 (mtt) REVERT: B 1380 ILE cc_start: 0.1375 (OUTLIER) cc_final: 0.1107 (pp) outliers start: 29 outliers final: 13 residues processed: 312 average time/residue: 0.6770 time to fit residues: 234.7099 Evaluate side-chains 203 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 1380 ILE Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1571 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 427 HIS A 719 GLN ** A1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 ASN B 449 ASN B 670 ASN B 862 GLN B 925 ASN B1169 GLN B1219 ASN B1230 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.166452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122064 restraints weight = 23643.069| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.14 r_work: 0.3117 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18752 Z= 0.265 Angle : 0.637 8.399 25282 Z= 0.331 Chirality : 0.047 0.181 2772 Planarity : 0.005 0.042 3188 Dihedral : 7.568 89.705 2488 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.47 % Allowed : 20.97 % Favored : 74.56 % 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: 1.26 (0.18), residues: 2186 helix: 1.53 (0.15), residues: 1228 sheet: 0.79 (0.35), residues: 210 loop : -0.24 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1529 TYR 0.024 0.002 TYR B1093 PHE 0.019 0.002 PHE B 583 TRP 0.010 0.002 TRP B 586 HIS 0.007 0.002 HIS A1494 Details of bonding type rmsd covalent geometry : bond 0.00645 (18752) covalent geometry : angle 0.63716 (25282) hydrogen bonds : bond 0.05845 ( 954) hydrogen bonds : angle 4.74289 ( 2757) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 186 time to evaluate : 0.780 Fit side-chains REVERT: A 506 LYS cc_start: 0.8632 (pttt) cc_final: 0.8266 (mptt) REVERT: A 509 ASP cc_start: 0.8090 (p0) cc_final: 0.7601 (p0) REVERT: A 536 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8346 (ptp90) REVERT: A 728 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7719 (t) REVERT: A 788 ARG cc_start: 0.8683 (ttm110) cc_final: 0.8477 (ttm110) REVERT: A 820 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7472 (mptt) REVERT: A 994 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8422 (mt-10) REVERT: A 997 LYS cc_start: 0.8319 (tttt) cc_final: 0.8109 (tptp) REVERT: A 1284 ILE cc_start: 0.6127 (OUTLIER) cc_final: 0.5554 (tt) REVERT: A 1342 ASP cc_start: 0.8066 (t0) cc_final: 0.7608 (p0) REVERT: A 1368 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: A 1465 LYS cc_start: 0.8824 (tttm) cc_final: 0.8327 (tppt) REVERT: A 1527 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6040 (mm) REVERT: A 1554 THR cc_start: 0.8329 (m) cc_final: 0.8128 (p) REVERT: B 478 GLU cc_start: 0.7134 (pm20) cc_final: 0.6855 (tp30) REVERT: B 509 ASP cc_start: 0.6861 (p0) cc_final: 0.6390 (p0) REVERT: B 553 ARG cc_start: 0.6490 (mtp-110) cc_final: 0.5799 (mtm-85) REVERT: B 713 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8189 (mtp180) REVERT: B 803 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: B 804 GLN cc_start: 0.8535 (mp10) cc_final: 0.7984 (mm-40) REVERT: B 820 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7461 (mtpt) REVERT: B 824 ARG cc_start: 0.8089 (mmt-90) cc_final: 0.7450 (mmp-170) REVERT: B 860 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8541 (ptpt) REVERT: B 903 ASN cc_start: 0.8545 (m-40) cc_final: 0.8186 (t0) REVERT: B 955 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7452 (tptp) REVERT: B 995 GLU cc_start: 0.8167 (tp30) cc_final: 0.7768 (tp30) REVERT: B 1107 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8635 (mtmt) REVERT: B 1111 ILE cc_start: 0.8476 (mt) cc_final: 0.8174 (pt) REVERT: B 1115 ASP cc_start: 0.8072 (t0) cc_final: 0.7850 (t0) REVERT: B 1165 GLU cc_start: 0.7065 (tt0) cc_final: 0.6743 (mm-30) REVERT: B 1269 ASP cc_start: 0.6395 (m-30) cc_final: 0.5963 (p0) REVERT: B 1282 ASN cc_start: 0.5925 (OUTLIER) cc_final: 0.5270 (t0) REVERT: B 1289 GLU cc_start: 0.4782 (OUTLIER) cc_final: 0.3572 (mm-30) REVERT: B 1427 GLN cc_start: 0.4707 (OUTLIER) cc_final: 0.4223 (tt0) outliers start: 91 outliers final: 32 residues processed: 262 average time/residue: 0.7047 time to fit residues: 204.8406 Evaluate side-chains 208 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 612 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 809 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1368 GLU Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1501 CYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1110 LYS Chi-restraints excluded: chain B residue 1282 ASN Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1427 GLN Chi-restraints excluded: chain B residue 1531 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 123 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 719 GLN A1064 ASN A1212 GLN A1219 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.166851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109992 restraints weight = 24193.904| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.83 r_work: 0.3216 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18752 Z= 0.144 Angle : 0.522 8.189 25282 Z= 0.272 Chirality : 0.043 0.156 2772 Planarity : 0.004 0.038 3188 Dihedral : 7.218 71.305 2480 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.83 % Allowed : 21.86 % Favored : 74.31 % 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: 1.47 (0.18), residues: 2186 helix: 1.74 (0.15), residues: 1228 sheet: 0.91 (0.35), residues: 206 loop : -0.21 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1529 TYR 0.018 0.001 TYR A1093 PHE 0.015 0.001 PHE B1099 TRP 0.010 0.001 TRP B 586 HIS 0.003 0.001 HIS A1076 Details of bonding type rmsd covalent geometry : bond 0.00341 (18752) covalent geometry : angle 0.52228 (25282) hydrogen bonds : bond 0.04409 ( 954) hydrogen bonds : angle 4.42788 ( 2757) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 182 time to evaluate : 0.647 Fit side-chains REVERT: A 506 LYS cc_start: 0.8498 (pttt) cc_final: 0.8183 (mptt) REVERT: A 509 ASP cc_start: 0.8040 (p0) cc_final: 0.7465 (p0) REVERT: A 536 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8287 (ptp90) REVERT: A 712 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: A 728 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7691 (t) REVERT: A 820 LYS cc_start: 0.7700 (ttmm) cc_final: 0.7379 (mptt) REVERT: A 843 LYS cc_start: 0.8512 (ttpt) cc_final: 0.7916 (ttmt) REVERT: A 1068 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: A 1284 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5701 (pp) REVERT: A 1342 ASP cc_start: 0.7929 (t0) cc_final: 0.7495 (p0) REVERT: A 1368 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: A 1374 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4910 (pp20) REVERT: A 1453 MET cc_start: 0.6653 (mmm) cc_final: 0.5429 (mpp) REVERT: A 1465 LYS cc_start: 0.8673 (tttm) cc_final: 0.8226 (mppt) REVERT: B 478 GLU cc_start: 0.6904 (pm20) cc_final: 0.6551 (tp30) REVERT: B 509 ASP cc_start: 0.6669 (p0) cc_final: 0.6249 (p0) REVERT: B 553 ARG cc_start: 0.6492 (mtp-110) cc_final: 0.5774 (mtm-85) REVERT: B 565 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: B 803 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7051 (OUTLIER) REVERT: B 804 GLN cc_start: 0.8316 (mp10) cc_final: 0.7825 (mm-40) REVERT: B 820 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7412 (mtpt) REVERT: B 824 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7314 (mmp-170) REVERT: B 903 ASN cc_start: 0.8308 (m-40) cc_final: 0.8007 (t0) REVERT: B 955 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7356 (tttp) REVERT: B 995 GLU cc_start: 0.7920 (tp30) cc_final: 0.7548 (tp30) REVERT: B 1111 ILE cc_start: 0.8372 (mt) cc_final: 0.8099 (pt) REVERT: B 1165 GLU cc_start: 0.6913 (tt0) cc_final: 0.6601 (mm-30) REVERT: B 1269 ASP cc_start: 0.6344 (m-30) cc_final: 0.5965 (p0) REVERT: B 1289 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.3567 (mm-30) REVERT: B 1427 GLN cc_start: 0.4763 (OUTLIER) cc_final: 0.4272 (tt0) REVERT: B 1448 GLN cc_start: 0.0151 (OUTLIER) cc_final: -0.0232 (tp40) outliers start: 78 outliers final: 29 residues processed: 245 average time/residue: 0.6794 time to fit residues: 184.8282 Evaluate side-chains 206 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 719 GLN 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 962 THR Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1170 SER Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1368 GLU Chi-restraints excluded: chain A residue 1374 GLU Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 974 GLU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1427 GLN Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1582 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 50 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 719 GLN A 839 GLN A1064 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.167442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110671 restraints weight = 24226.866| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.83 r_work: 0.3228 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18752 Z= 0.123 Angle : 0.490 8.339 25282 Z= 0.255 Chirality : 0.042 0.162 2772 Planarity : 0.004 0.038 3188 Dihedral : 6.997 68.780 2480 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.63 % Allowed : 22.35 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.18), residues: 2186 helix: 1.89 (0.15), residues: 1228 sheet: 0.88 (0.35), residues: 206 loop : -0.16 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 788 TYR 0.018 0.001 TYR A1093 PHE 0.012 0.001 PHE B 675 TRP 0.009 0.001 TRP B 586 HIS 0.003 0.001 HIS A1076 Details of bonding type rmsd covalent geometry : bond 0.00285 (18752) covalent geometry : angle 0.48996 (25282) hydrogen bonds : bond 0.03902 ( 954) hydrogen bonds : angle 4.24204 ( 2757) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 172 time to evaluate : 0.718 Fit side-chains REVERT: A 506 LYS cc_start: 0.8507 (pttt) cc_final: 0.8193 (mptt) REVERT: A 509 ASP cc_start: 0.7969 (p0) cc_final: 0.7386 (p0) REVERT: A 536 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8302 (ptp90) REVERT: A 728 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7676 (t) REVERT: A 820 LYS cc_start: 0.7681 (ttmm) cc_final: 0.7363 (mptt) REVERT: A 843 LYS cc_start: 0.8480 (ttpt) cc_final: 0.7864 (ttmt) REVERT: A 1068 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: A 1284 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5751 (pp) REVERT: A 1342 ASP cc_start: 0.7934 (t0) cc_final: 0.7481 (p0) REVERT: A 1461 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6585 (mppt) REVERT: A 1465 LYS cc_start: 0.8644 (tttm) cc_final: 0.8190 (mppt) REVERT: B 509 ASP cc_start: 0.6703 (p0) cc_final: 0.6286 (p0) REVERT: B 523 LYS cc_start: 0.7844 (mtpt) cc_final: 0.6911 (mmpt) REVERT: B 553 ARG cc_start: 0.6521 (mtp-110) cc_final: 0.5805 (mtm-85) REVERT: B 565 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: B 803 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7075 (OUTLIER) REVERT: B 804 GLN cc_start: 0.8344 (mp10) cc_final: 0.7852 (mm-40) REVERT: B 820 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7410 (mtpt) REVERT: B 824 ARG cc_start: 0.7965 (mmt-90) cc_final: 0.7318 (mmp-170) REVERT: B 903 ASN cc_start: 0.8284 (m-40) cc_final: 0.7965 (t0) REVERT: B 995 GLU cc_start: 0.7893 (tp30) cc_final: 0.7536 (tp30) REVERT: B 1088 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7853 (tt) REVERT: B 1111 ILE cc_start: 0.8397 (mt) cc_final: 0.8132 (pt) REVERT: B 1165 GLU cc_start: 0.6897 (tt0) cc_final: 0.6577 (mm-30) REVERT: B 1269 ASP cc_start: 0.6334 (m-30) cc_final: 0.5943 (p0) REVERT: B 1282 ASN cc_start: 0.5829 (m-40) cc_final: 0.5366 (t0) REVERT: B 1289 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.3670 (mm-30) REVERT: B 1333 ARG cc_start: 0.4671 (OUTLIER) cc_final: 0.4103 (mtp-110) REVERT: B 1448 GLN cc_start: 0.0016 (OUTLIER) cc_final: -0.0329 (tp40) outliers start: 74 outliers final: 34 residues processed: 234 average time/residue: 0.6777 time to fit residues: 176.3810 Evaluate side-chains 201 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 612 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 965 THR Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1147 ASP Chi-restraints excluded: chain A residue 1170 SER Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1251 LYS Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1501 CYS Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 974 GLU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 LYS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1582 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A1064 ASN B 565 GLN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109632 restraints weight = 24237.802| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.31 r_work: 0.3121 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18752 Z= 0.212 Angle : 0.567 10.822 25282 Z= 0.293 Chirality : 0.045 0.228 2772 Planarity : 0.004 0.041 3188 Dihedral : 7.287 70.086 2480 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.47 % Allowed : 21.41 % Favored : 74.12 % 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: 1.34 (0.18), residues: 2186 helix: 1.66 (0.15), residues: 1228 sheet: 0.72 (0.35), residues: 206 loop : -0.27 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 788 TYR 0.022 0.002 TYR A1093 PHE 0.015 0.002 PHE B 675 TRP 0.011 0.001 TRP B1134 HIS 0.006 0.001 HIS A1494 Details of bonding type rmsd covalent geometry : bond 0.00520 (18752) covalent geometry : angle 0.56698 (25282) hydrogen bonds : bond 0.04888 ( 954) hydrogen bonds : angle 4.35865 ( 2757) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 171 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 LYS cc_start: 0.8552 (pttt) cc_final: 0.8187 (mptt) REVERT: A 509 ASP cc_start: 0.8099 (p0) cc_final: 0.7521 (p0) REVERT: A 536 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8433 (ptp90) REVERT: A 712 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: A 820 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7414 (mptt) REVERT: A 843 LYS cc_start: 0.8536 (ttpt) cc_final: 0.7889 (ttmt) REVERT: A 1068 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: A 1284 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.5930 (pp) REVERT: A 1342 ASP cc_start: 0.8078 (t0) cc_final: 0.7618 (p0) REVERT: A 1427 GLN cc_start: 0.7044 (pm20) cc_final: 0.6801 (pp30) REVERT: A 1461 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6838 (mppt) REVERT: A 1465 LYS cc_start: 0.8711 (tttm) cc_final: 0.8230 (mppt) REVERT: B 509 ASP cc_start: 0.6811 (p0) cc_final: 0.6378 (p0) REVERT: B 523 LYS cc_start: 0.7913 (mtpt) cc_final: 0.6952 (mmpt) REVERT: B 553 ARG cc_start: 0.6474 (mtp-110) cc_final: 0.5798 (mtm-85) REVERT: B 565 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: B 803 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7276 (pt0) REVERT: B 804 GLN cc_start: 0.8558 (mp10) cc_final: 0.8093 (mm-40) REVERT: B 820 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7467 (mtpt) REVERT: B 824 ARG cc_start: 0.7936 (mmt-90) cc_final: 0.7352 (mmp-170) REVERT: B 860 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8559 (ptpt) REVERT: B 903 ASN cc_start: 0.8420 (m-40) cc_final: 0.8031 (t0) REVERT: B 995 GLU cc_start: 0.8040 (tp30) cc_final: 0.7643 (tp30) REVERT: B 1088 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7904 (tt) REVERT: B 1111 ILE cc_start: 0.8447 (mt) cc_final: 0.8166 (pt) REVERT: B 1165 GLU cc_start: 0.6916 (tt0) cc_final: 0.6664 (mm-30) REVERT: B 1269 ASP cc_start: 0.6380 (m-30) cc_final: 0.5918 (p0) REVERT: B 1282 ASN cc_start: 0.6016 (m-40) cc_final: 0.5422 (t0) REVERT: B 1289 GLU cc_start: 0.5124 (OUTLIER) cc_final: 0.3741 (mm-30) REVERT: B 1333 ARG cc_start: 0.4710 (OUTLIER) cc_final: 0.4178 (mtp-110) REVERT: B 1426 TYR cc_start: -0.0640 (OUTLIER) cc_final: -0.1119 (t80) REVERT: B 1427 GLN cc_start: 0.4605 (OUTLIER) cc_final: 0.4240 (tt0) REVERT: B 1448 GLN cc_start: -0.0040 (OUTLIER) cc_final: -0.0421 (tp40) outliers start: 91 outliers final: 40 residues processed: 243 average time/residue: 0.6629 time to fit residues: 179.3281 Evaluate side-chains 216 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 712 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 824 ARG Chi-restraints excluded: chain A residue 860 LYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1170 SER Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1251 LYS Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1501 CYS Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 565 GLN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 974 GLU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 LYS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1224 SER Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1427 GLN Chi-restraints excluded: chain B residue 1448 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 17 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 840 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111054 restraints weight = 24132.183| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.09 r_work: 0.3184 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18752 Z= 0.134 Angle : 0.504 8.734 25282 Z= 0.261 Chirality : 0.042 0.245 2772 Planarity : 0.004 0.040 3188 Dihedral : 7.020 72.370 2480 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.49 % Allowed : 22.45 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.18), residues: 2186 helix: 1.84 (0.15), residues: 1228 sheet: 0.85 (0.35), residues: 202 loop : -0.24 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 788 TYR 0.019 0.001 TYR A1093 PHE 0.015 0.001 PHE A1262 TRP 0.010 0.001 TRP B 586 HIS 0.004 0.001 HIS A1076 Details of bonding type rmsd covalent geometry : bond 0.00316 (18752) covalent geometry : angle 0.50437 (25282) hydrogen bonds : bond 0.03972 ( 954) hydrogen bonds : angle 4.19226 ( 2757) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 167 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 506 LYS cc_start: 0.8442 (pttt) cc_final: 0.8047 (mptt) REVERT: A 509 ASP cc_start: 0.7974 (p0) cc_final: 0.7334 (p0) REVERT: A 536 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8328 (ptp90) REVERT: A 712 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: A 820 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7236 (mptt) REVERT: A 843 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7718 (ttmt) REVERT: A 1068 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: A 1284 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.5910 (pp) REVERT: A 1342 ASP cc_start: 0.7932 (t0) cc_final: 0.7426 (p0) REVERT: A 1427 GLN cc_start: 0.6938 (pm20) cc_final: 0.6702 (pp30) REVERT: A 1461 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6514 (mppt) REVERT: A 1465 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8055 (mppt) REVERT: A 1524 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6363 (pm20) REVERT: B 509 ASP cc_start: 0.6655 (p0) cc_final: 0.6205 (p0) REVERT: B 523 LYS cc_start: 0.7668 (mtpt) cc_final: 0.6707 (mmpt) REVERT: B 553 ARG cc_start: 0.6360 (mtp-110) cc_final: 0.5689 (mtm-85) REVERT: B 565 GLN cc_start: 0.8005 (mp10) cc_final: 0.7578 (tt0) REVERT: B 803 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7136 (pt0) REVERT: B 804 GLN cc_start: 0.8476 (mp10) cc_final: 0.7921 (mm-40) REVERT: B 820 LYS cc_start: 0.7675 (ttmm) cc_final: 0.7336 (mtpt) REVERT: B 824 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7310 (mmp-170) REVERT: B 903 ASN cc_start: 0.8227 (m-40) cc_final: 0.7844 (t0) REVERT: B 995 GLU cc_start: 0.7837 (tp30) cc_final: 0.7429 (tp30) REVERT: B 1088 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7627 (tt) REVERT: B 1165 GLU cc_start: 0.6758 (tt0) cc_final: 0.6437 (mm-30) REVERT: B 1269 ASP cc_start: 0.6274 (m-30) cc_final: 0.5887 (p0) REVERT: B 1282 ASN cc_start: 0.5956 (m-40) cc_final: 0.5455 (t0) REVERT: B 1289 GLU cc_start: 0.5043 (OUTLIER) cc_final: 0.3678 (mm-30) REVERT: B 1333 ARG cc_start: 0.4698 (OUTLIER) cc_final: 0.4136 (mtp-110) REVERT: B 1426 TYR cc_start: -0.0513 (OUTLIER) cc_final: -0.0933 (t80) REVERT: B 1427 GLN cc_start: 0.4456 (OUTLIER) cc_final: 0.4199 (tt0) REVERT: B 1448 GLN cc_start: -0.0084 (OUTLIER) cc_final: -0.0433 (tp40) outliers start: 71 outliers final: 31 residues processed: 224 average time/residue: 0.6654 time to fit residues: 166.1398 Evaluate side-chains 208 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 712 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 962 THR Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1170 SER Chi-restraints excluded: chain A residue 1200 GLU Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 974 GLU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 LYS Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1427 GLN Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1474 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 23 optimal weight: 0.0270 chunk 110 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 203 optimal weight: 0.0870 chunk 201 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 221 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 171 optimal weight: 0.2980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 840 ASN A1143 ASN B1169 GLN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113544 restraints weight = 24266.293| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.81 r_work: 0.3263 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18752 Z= 0.089 Angle : 0.463 11.318 25282 Z= 0.239 Chirality : 0.040 0.153 2772 Planarity : 0.003 0.038 3188 Dihedral : 6.545 80.108 2478 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.36 % Allowed : 23.87 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.91 (0.18), residues: 2186 helix: 2.15 (0.15), residues: 1232 sheet: 0.98 (0.37), residues: 190 loop : -0.07 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1188 TYR 0.015 0.001 TYR A1093 PHE 0.011 0.001 PHE A1388 TRP 0.008 0.001 TRP B 586 HIS 0.004 0.001 HIS A1076 Details of bonding type rmsd covalent geometry : bond 0.00184 (18752) covalent geometry : angle 0.46277 (25282) hydrogen bonds : bond 0.02974 ( 954) hydrogen bonds : angle 3.97991 ( 2757) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 LYS cc_start: 0.8470 (pttt) cc_final: 0.8174 (mptt) REVERT: A 509 ASP cc_start: 0.7993 (p0) cc_final: 0.7345 (p0) REVERT: A 786 MET cc_start: 0.7465 (mmm) cc_final: 0.7210 (mmt) REVERT: A 820 LYS cc_start: 0.7594 (ttmm) cc_final: 0.7308 (mptt) REVERT: A 843 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7781 (ttmt) REVERT: A 1060 LYS cc_start: 0.8858 (tttt) cc_final: 0.8498 (tttp) REVERT: A 1068 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: A 1284 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5876 (pp) REVERT: A 1342 ASP cc_start: 0.7803 (t0) cc_final: 0.7440 (p0) REVERT: A 1461 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6580 (mppt) REVERT: A 1465 LYS cc_start: 0.8555 (tttm) cc_final: 0.8106 (mppt) REVERT: A 1528 LEU cc_start: 0.6709 (tt) cc_final: 0.6443 (tm) REVERT: B 509 ASP cc_start: 0.6595 (p0) cc_final: 0.6220 (p0) REVERT: B 523 LYS cc_start: 0.7801 (mtpt) cc_final: 0.6892 (mmpt) REVERT: B 553 ARG cc_start: 0.6461 (mtp-110) cc_final: 0.5799 (mtm-85) REVERT: B 565 GLN cc_start: 0.8101 (mp10) cc_final: 0.7743 (tt0) REVERT: B 803 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7243 (OUTLIER) REVERT: B 804 GLN cc_start: 0.8467 (mp10) cc_final: 0.7951 (mm-40) REVERT: B 820 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7457 (mtpt) REVERT: B 824 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7285 (mmp-170) REVERT: B 903 ASN cc_start: 0.8179 (m-40) cc_final: 0.7883 (t0) REVERT: B 995 GLU cc_start: 0.7804 (tp30) cc_final: 0.7434 (tp30) REVERT: B 1088 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7789 (tt) REVERT: B 1165 GLU cc_start: 0.6873 (tt0) cc_final: 0.6531 (mm-30) REVERT: B 1269 ASP cc_start: 0.6271 (m-30) cc_final: 0.5942 (p0) REVERT: B 1282 ASN cc_start: 0.5958 (m-40) cc_final: 0.5581 (t0) REVERT: B 1289 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.3661 (mm-30) REVERT: B 1334 ARG cc_start: 0.3314 (OUTLIER) cc_final: 0.2037 (tmm160) REVERT: B 1426 TYR cc_start: -0.0535 (OUTLIER) cc_final: -0.0967 (t80) outliers start: 48 outliers final: 20 residues processed: 223 average time/residue: 0.6455 time to fit residues: 161.2017 Evaluate side-chains 194 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain A residue 1147 ASP Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1334 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1474 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN A1143 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110039 restraints weight = 24339.434| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.78 r_work: 0.3214 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18752 Z= 0.151 Angle : 0.516 10.990 25282 Z= 0.264 Chirality : 0.043 0.317 2772 Planarity : 0.004 0.038 3188 Dihedral : 6.698 74.708 2472 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.50 % Allowed : 23.82 % Favored : 73.67 % 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: 1.73 (0.18), residues: 2186 helix: 2.01 (0.15), residues: 1228 sheet: 0.87 (0.35), residues: 202 loop : -0.16 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1188 TYR 0.019 0.001 TYR A1093 PHE 0.013 0.001 PHE B 675 TRP 0.019 0.001 TRP B1134 HIS 0.004 0.001 HIS A1494 Details of bonding type rmsd covalent geometry : bond 0.00367 (18752) covalent geometry : angle 0.51562 (25282) hydrogen bonds : bond 0.04011 ( 954) hydrogen bonds : angle 4.09910 ( 2757) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 506 LYS cc_start: 0.8490 (pttt) cc_final: 0.8179 (mptt) REVERT: A 509 ASP cc_start: 0.7976 (p0) cc_final: 0.7378 (p0) REVERT: A 536 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8257 (ptp90) REVERT: A 820 LYS cc_start: 0.7640 (ttmm) cc_final: 0.7360 (mptt) REVERT: A 843 LYS cc_start: 0.8438 (ttpt) cc_final: 0.7829 (ttmt) REVERT: A 1060 LYS cc_start: 0.8866 (tttt) cc_final: 0.8523 (tttp) REVERT: A 1342 ASP cc_start: 0.7924 (t0) cc_final: 0.7576 (p0) REVERT: A 1427 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6468 (pp30) REVERT: A 1461 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6639 (mppt) REVERT: A 1465 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8164 (mppt) REVERT: A 1524 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: A 1528 LEU cc_start: 0.6748 (tt) cc_final: 0.6517 (tm) REVERT: A 1585 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7203 (m-30) REVERT: B 509 ASP cc_start: 0.6708 (p0) cc_final: 0.6301 (p0) REVERT: B 523 LYS cc_start: 0.7837 (mtpt) cc_final: 0.6920 (mmpt) REVERT: B 553 ARG cc_start: 0.6444 (mtp-110) cc_final: 0.5788 (mtm-85) REVERT: B 565 GLN cc_start: 0.8098 (mp10) cc_final: 0.7751 (tt0) REVERT: B 803 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: B 804 GLN cc_start: 0.8540 (mp10) cc_final: 0.8069 (mm-40) REVERT: B 820 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7478 (mtpt) REVERT: B 824 ARG cc_start: 0.7860 (mmt-90) cc_final: 0.7282 (mmp-170) REVERT: B 903 ASN cc_start: 0.8301 (m-40) cc_final: 0.7953 (t0) REVERT: B 995 GLU cc_start: 0.7875 (tp30) cc_final: 0.7478 (tp30) REVERT: B 1088 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7788 (tt) REVERT: B 1110 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7138 (mmtp) REVERT: B 1165 GLU cc_start: 0.6958 (tt0) cc_final: 0.6631 (mm-30) REVERT: B 1269 ASP cc_start: 0.6395 (m-30) cc_final: 0.5917 (p0) REVERT: B 1282 ASN cc_start: 0.6070 (m-40) cc_final: 0.5583 (t0) REVERT: B 1289 GLU cc_start: 0.5114 (OUTLIER) cc_final: 0.3746 (mm-30) REVERT: B 1333 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.4266 (mtp-110) REVERT: B 1426 TYR cc_start: -0.0480 (OUTLIER) cc_final: -0.1036 (t80) REVERT: B 1448 GLN cc_start: 0.0082 (OUTLIER) cc_final: -0.0279 (tp40) outliers start: 51 outliers final: 25 residues processed: 211 average time/residue: 0.7192 time to fit residues: 168.7738 Evaluate side-chains 202 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1427 GLN Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1469 LYS Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 LYS Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1334 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1474 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 121 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 0.0870 chunk 135 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 840 ASN A1143 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.166764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111123 restraints weight = 24202.219| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.79 r_work: 0.3226 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18752 Z= 0.120 Angle : 0.493 11.466 25282 Z= 0.254 Chirality : 0.042 0.280 2772 Planarity : 0.003 0.038 3188 Dihedral : 6.538 75.999 2470 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.16 % Allowed : 24.36 % Favored : 73.48 % 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: 1.76 (0.18), residues: 2186 helix: 2.04 (0.15), residues: 1228 sheet: 1.04 (0.37), residues: 186 loop : -0.21 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1188 TYR 0.018 0.001 TYR A1093 PHE 0.014 0.001 PHE A1262 TRP 0.023 0.001 TRP B1134 HIS 0.003 0.001 HIS A1494 Details of bonding type rmsd covalent geometry : bond 0.00281 (18752) covalent geometry : angle 0.49347 (25282) hydrogen bonds : bond 0.03567 ( 954) hydrogen bonds : angle 4.05419 ( 2757) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.691 Fit side-chains REVERT: A 506 LYS cc_start: 0.8483 (pttt) cc_final: 0.8183 (mptt) REVERT: A 509 ASP cc_start: 0.8007 (p0) cc_final: 0.7382 (p0) REVERT: A 536 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8263 (ptp90) REVERT: A 820 LYS cc_start: 0.7633 (ttmm) cc_final: 0.7353 (mptt) REVERT: A 843 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7809 (ttmt) REVERT: A 1060 LYS cc_start: 0.8875 (tttt) cc_final: 0.8518 (tttp) REVERT: A 1342 ASP cc_start: 0.7932 (t0) cc_final: 0.7602 (p0) REVERT: A 1427 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6497 (pp30) REVERT: A 1461 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6597 (mppt) REVERT: A 1465 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8154 (mppt) REVERT: A 1524 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: A 1528 LEU cc_start: 0.6685 (tt) cc_final: 0.6478 (tm) REVERT: A 1585 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: B 509 ASP cc_start: 0.6720 (p0) cc_final: 0.6318 (p0) REVERT: B 523 LYS cc_start: 0.7827 (mtpt) cc_final: 0.6919 (mmpt) REVERT: B 553 ARG cc_start: 0.6424 (mtp-110) cc_final: 0.5805 (mtm-85) REVERT: B 565 GLN cc_start: 0.8112 (mp10) cc_final: 0.7755 (tt0) REVERT: B 803 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: B 804 GLN cc_start: 0.8534 (mp10) cc_final: 0.8091 (mm-40) REVERT: B 820 LYS cc_start: 0.7805 (ttmm) cc_final: 0.7486 (mtpt) REVERT: B 824 ARG cc_start: 0.7852 (mmt-90) cc_final: 0.7281 (mmp-170) REVERT: B 903 ASN cc_start: 0.8250 (m-40) cc_final: 0.7928 (t0) REVERT: B 995 GLU cc_start: 0.7846 (tp30) cc_final: 0.7464 (tp30) REVERT: B 1088 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7777 (tt) REVERT: B 1110 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7000 (mmtp) REVERT: B 1165 GLU cc_start: 0.6912 (tt0) cc_final: 0.6566 (mm-30) REVERT: B 1269 ASP cc_start: 0.6341 (m-30) cc_final: 0.5922 (p0) REVERT: B 1282 ASN cc_start: 0.6071 (m-40) cc_final: 0.5632 (t0) REVERT: B 1289 GLU cc_start: 0.5108 (OUTLIER) cc_final: 0.3734 (mm-30) REVERT: B 1333 ARG cc_start: 0.4841 (OUTLIER) cc_final: 0.4267 (mtp-110) REVERT: B 1334 ARG cc_start: 0.3513 (OUTLIER) cc_final: 0.2168 (tmm160) REVERT: B 1426 TYR cc_start: -0.0529 (OUTLIER) cc_final: -0.1127 (t80) REVERT: B 1448 GLN cc_start: 0.0066 (OUTLIER) cc_final: -0.0297 (tp40) outliers start: 44 outliers final: 22 residues processed: 204 average time/residue: 0.6858 time to fit residues: 155.7951 Evaluate side-chains 198 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP 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 824 ARG Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1396 SER Chi-restraints excluded: chain A residue 1427 GLN Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1585 ASP Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 LYS Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1334 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 186 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN A1143 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112976 restraints weight = 24307.268| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.21 r_work: 0.3202 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18752 Z= 0.116 Angle : 0.500 13.642 25282 Z= 0.255 Chirality : 0.042 0.262 2772 Planarity : 0.003 0.038 3188 Dihedral : 6.506 77.444 2470 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.06 % Allowed : 24.56 % Favored : 73.38 % 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: 1.79 (0.18), residues: 2186 helix: 2.07 (0.15), residues: 1228 sheet: 1.04 (0.37), residues: 186 loop : -0.18 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1188 TYR 0.017 0.001 TYR A1093 PHE 0.011 0.001 PHE B 675 TRP 0.029 0.001 TRP B1134 HIS 0.003 0.001 HIS A1494 Details of bonding type rmsd covalent geometry : bond 0.00270 (18752) covalent geometry : angle 0.50025 (25282) hydrogen bonds : bond 0.03531 ( 954) hydrogen bonds : angle 4.02309 ( 2757) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 506 LYS cc_start: 0.8482 (pttt) cc_final: 0.8157 (mptt) REVERT: A 509 ASP cc_start: 0.8018 (p0) cc_final: 0.7376 (p0) REVERT: A 536 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8326 (ptp90) REVERT: A 786 MET cc_start: 0.7491 (mmm) cc_final: 0.7243 (mmt) REVERT: A 820 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7353 (mptt) REVERT: A 843 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7803 (ttmt) REVERT: A 1060 LYS cc_start: 0.8893 (tttt) cc_final: 0.8542 (tttp) REVERT: A 1342 ASP cc_start: 0.7963 (t0) cc_final: 0.7661 (p0) REVERT: A 1427 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6551 (pp30) REVERT: A 1461 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6658 (mppt) REVERT: A 1465 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8145 (mppt) REVERT: A 1528 LEU cc_start: 0.6733 (tt) cc_final: 0.6517 (tm) REVERT: B 475 THR cc_start: 0.7008 (p) cc_final: 0.6776 (p) REVERT: B 509 ASP cc_start: 0.6718 (p0) cc_final: 0.6309 (p0) REVERT: B 523 LYS cc_start: 0.7847 (mtpt) cc_final: 0.6941 (mmpt) REVERT: B 553 ARG cc_start: 0.6452 (mtp-110) cc_final: 0.5809 (mtm-85) REVERT: B 803 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: B 804 GLN cc_start: 0.8558 (mp10) cc_final: 0.8046 (mm-40) REVERT: B 820 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7488 (mtpt) REVERT: B 824 ARG cc_start: 0.7876 (mmt-90) cc_final: 0.7300 (mmp-170) REVERT: B 903 ASN cc_start: 0.8272 (m-40) cc_final: 0.7925 (t0) REVERT: B 995 GLU cc_start: 0.7917 (tp30) cc_final: 0.7546 (tp30) REVERT: B 1088 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7811 (tt) REVERT: B 1110 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7000 (mmtp) REVERT: B 1165 GLU cc_start: 0.6959 (tt0) cc_final: 0.6619 (mm-30) REVERT: B 1269 ASP cc_start: 0.6374 (m-30) cc_final: 0.5914 (p0) REVERT: B 1282 ASN cc_start: 0.6033 (m-40) cc_final: 0.5601 (t0) REVERT: B 1289 GLU cc_start: 0.5213 (OUTLIER) cc_final: 0.3760 (mm-30) REVERT: B 1333 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4309 (mtp-110) REVERT: B 1334 ARG cc_start: 0.3563 (OUTLIER) cc_final: 0.2189 (tmm160) REVERT: B 1426 TYR cc_start: -0.0481 (OUTLIER) cc_final: -0.1094 (t80) REVERT: B 1448 GLN cc_start: 0.0035 (OUTLIER) cc_final: -0.0319 (tp40) outliers start: 42 outliers final: 23 residues processed: 198 average time/residue: 0.6486 time to fit residues: 143.0141 Evaluate side-chains 195 residues out of total 2036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 551 ASP 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 824 ARG Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1427 GLN Chi-restraints excluded: chain A residue 1461 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 LYS Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1289 GLU Chi-restraints excluded: chain B residue 1333 ARG Chi-restraints excluded: chain B residue 1334 ARG Chi-restraints excluded: chain B residue 1426 TYR Chi-restraints excluded: chain B residue 1448 GLN Chi-restraints excluded: chain B residue 1474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 103 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 840 ASN A 925 ASN ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 834 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111330 restraints weight = 24332.271| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.05 r_work: 0.3146 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 18752 Z= 0.268 Angle : 0.620 14.058 25282 Z= 0.317 Chirality : 0.047 0.333 2772 Planarity : 0.004 0.040 3188 Dihedral : 7.133 69.792 2470 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.55 % Allowed : 24.26 % Favored : 73.18 % 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: 1.33 (0.18), residues: 2186 helix: 1.71 (0.15), residues: 1214 sheet: 0.59 (0.35), residues: 206 loop : -0.31 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1188 TYR 0.025 0.002 TYR A1093 PHE 0.018 0.002 PHE A1216 TRP 0.032 0.002 TRP B1134 HIS 0.009 0.001 HIS A1494 Details of bonding type rmsd covalent geometry : bond 0.00663 (18752) covalent geometry : angle 0.61970 (25282) hydrogen bonds : bond 0.05181 ( 954) hydrogen bonds : angle 4.32678 ( 2757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8257.25 seconds wall clock time: 141 minutes 6.40 seconds (8466.40 seconds total)