Starting phenix.real_space_refine on Sat Mar 7 04:39:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq1_32082/03_2026/7vq1_32082.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq1_32082/03_2026/7vq1_32082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq1_32082/03_2026/7vq1_32082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq1_32082/03_2026/7vq1_32082.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq1_32082/03_2026/7vq1_32082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq1_32082/03_2026/7vq1_32082.cif" } resolution = 3.76 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= 0.000 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: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 24384 2.51 5 N 6680 2.21 5 O 6592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.04s 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: 37804 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 9451 Classifications: {'peptide': 1302} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 62, 'TRANS': 1239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1095 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'GLU:plan': 48, 'PHE:plan': 11, 'ASP:plan': 33, 'HIS:plan': 10, 'TRP:plan': 5, 'ARG:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 711 Restraints were copied for chains: B, C, D Time building chain proxies: 12.44, per 1000 atoms: 0.33 Number of scatterers: 37804 At special positions: 0 Unit cell: (173.565, 174.42, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 6592 8.00 N 6680 7.00 C 24384 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: 3.79 Conformation dependent library (CDL) restraints added in 1.9 seconds 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9832 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 34 sheets defined 55.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.723A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.762A pdb=" N ARG A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.760A pdb=" N VAL A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.666A pdb=" N ASP A 453 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 530 through 542 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.997A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.684A pdb=" N ALA A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 Processing helix chain 'A' and resid 716 through 725 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 767 " --> pdb=" O PHE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.800A pdb=" N GLN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 794 through 819 Processing helix chain 'A' and resid 826 through 846 Processing helix chain 'A' and resid 855 through 866 Processing helix chain 'A' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 909 removed outlier: 3.532A pdb=" N ARG A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.519A pdb=" N ILE A 916 " --> pdb=" O ILE A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 956 removed outlier: 4.684A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 979 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.658A pdb=" N ASN A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE A1062 " --> pdb=" O HIS A1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP A1069 " --> pdb=" O PHE A1065 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A1070 " --> pdb=" O GLN A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A1095 " --> pdb=" O GLN A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1141 Processing helix chain 'A' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ALA A1157 " --> pdb=" O ASN A1153 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP A1291 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1403 Processing helix chain 'A' and resid 1410 through 1419 Processing helix chain 'A' and resid 1454 through 1463 Processing helix chain 'A' and resid 1485 through 1498 removed outlier: 3.691A pdb=" N LYS A1489 " --> pdb=" O TYR A1485 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A1490 " --> pdb=" O ALA A1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.725A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.761A pdb=" N ARG B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.761A pdb=" N VAL B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 363 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 444 Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.667A pdb=" N ASP B 453 " --> pdb=" O HIS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 530 through 542 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 557 through 570 removed outlier: 3.998A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.684A pdb=" N ALA B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 663 Processing helix chain 'B' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 705 Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 733 through 744 Processing helix chain 'B' and resid 753 through 762 Processing helix chain 'B' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU B 766 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 767 " --> pdb=" O PHE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.801A pdb=" N GLN B 779 " --> pdb=" O GLU B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 Processing helix chain 'B' and resid 794 through 819 Processing helix chain 'B' and resid 826 through 846 Processing helix chain 'B' and resid 855 through 866 Processing helix chain 'B' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR B 884 " --> pdb=" O VAL B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 909 removed outlier: 3.533A pdb=" N ARG B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.519A pdb=" N ILE B 916 " --> pdb=" O ILE B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 956 removed outlier: 4.683A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 979 Processing helix chain 'B' and resid 1021 through 1037 removed outlier: 3.658A pdb=" N ASN B1037 " --> pdb=" O LEU B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1056 Processing helix chain 'B' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE B1062 " --> pdb=" O HIS B1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS B1068 " --> pdb=" O LYS B1064 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP B1069 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER B1088 " --> pdb=" O PHE B1084 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS B1095 " --> pdb=" O GLN B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1141 Processing helix chain 'B' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ALA B1157 " --> pdb=" O ASN B1153 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP B1291 " --> pdb=" O PRO B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1398 through 1403 Processing helix chain 'B' and resid 1410 through 1419 Processing helix chain 'B' and resid 1454 through 1463 Processing helix chain 'B' and resid 1485 through 1498 removed outlier: 3.692A pdb=" N LYS B1489 " --> pdb=" O TYR B1485 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B1490 " --> pdb=" O ALA B1486 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.723A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.762A pdb=" N ARG C 304 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 357 through 367 removed outlier: 3.760A pdb=" N VAL C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 444 Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.666A pdb=" N ASP C 453 " --> pdb=" O HIS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 530 through 542 Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 557 through 570 removed outlier: 3.997A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.684A pdb=" N ALA C 643 " --> pdb=" O GLY C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 663 Processing helix chain 'C' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP C 697 " --> pdb=" O CYS C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 705 Processing helix chain 'C' and resid 716 through 725 Processing helix chain 'C' and resid 726 through 731 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 753 through 762 Processing helix chain 'C' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU C 766 " --> pdb=" O ALA C 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 767 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.800A pdb=" N GLN C 779 " --> pdb=" O GLU C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 Processing helix chain 'C' and resid 794 through 819 Processing helix chain 'C' and resid 826 through 846 Processing helix chain 'C' and resid 855 through 866 Processing helix chain 'C' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR C 884 " --> pdb=" O VAL C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 909 removed outlier: 3.532A pdb=" N ARG C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.519A pdb=" N ILE C 916 " --> pdb=" O ILE C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 956 removed outlier: 4.684A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 979 Processing helix chain 'C' and resid 1021 through 1037 removed outlier: 3.658A pdb=" N ASN C1037 " --> pdb=" O LEU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1056 Processing helix chain 'C' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE C1062 " --> pdb=" O HIS C1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS C1068 " --> pdb=" O LYS C1064 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP C1069 " --> pdb=" O PHE C1065 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER C1088 " --> pdb=" O PHE C1084 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS C1095 " --> pdb=" O GLN C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1141 Processing helix chain 'C' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ALA C1157 " --> pdb=" O ASN C1153 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP C1291 " --> pdb=" O PRO C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1398 through 1403 Processing helix chain 'C' and resid 1410 through 1419 Processing helix chain 'C' and resid 1454 through 1463 Processing helix chain 'C' and resid 1485 through 1498 removed outlier: 3.691A pdb=" N LYS C1489 " --> pdb=" O TYR C1485 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR C1490 " --> pdb=" O ALA C1486 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.724A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 201 removed outlier: 3.638A pdb=" N THR D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 229 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.762A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 Processing helix chain 'D' and resid 357 through 367 removed outlier: 3.761A pdb=" N VAL D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 363 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 388 Processing helix chain 'D' and resid 395 through 412 removed outlier: 3.911A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 444 Processing helix chain 'D' and resid 449 through 462 removed outlier: 3.666A pdb=" N ASP D 453 " --> pdb=" O HIS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 496 through 506 removed outlier: 3.740A pdb=" N VAL D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 515 through 523 Processing helix chain 'D' and resid 530 through 543 Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.998A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 4.006A pdb=" N ASP D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.683A pdb=" N ALA D 643 " --> pdb=" O GLY D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 663 Processing helix chain 'D' and resid 668 through 697 removed outlier: 3.612A pdb=" N GLU D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 697 " --> pdb=" O CYS D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 705 Processing helix chain 'D' and resid 716 through 725 Processing helix chain 'D' and resid 726 through 731 Processing helix chain 'D' and resid 733 through 744 Processing helix chain 'D' and resid 753 through 762 Processing helix chain 'D' and resid 762 through 768 removed outlier: 4.117A pdb=" N LEU D 766 " --> pdb=" O ALA D 762 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 767 " --> pdb=" O PHE D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.800A pdb=" N GLN D 779 " --> pdb=" O GLU D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 794 through 819 Processing helix chain 'D' and resid 826 through 846 Processing helix chain 'D' and resid 855 through 866 Processing helix chain 'D' and resid 866 through 888 removed outlier: 4.032A pdb=" N THR D 884 " --> pdb=" O VAL D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 909 removed outlier: 3.533A pdb=" N ARG D 909 " --> pdb=" O LEU D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 916 removed outlier: 3.518A pdb=" N ILE D 916 " --> pdb=" O ILE D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 956 removed outlier: 4.683A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 979 Processing helix chain 'D' and resid 1021 through 1037 removed outlier: 3.657A pdb=" N ASN D1037 " --> pdb=" O LEU D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1056 Processing helix chain 'D' and resid 1058 through 1077 removed outlier: 4.039A pdb=" N ILE D1062 " --> pdb=" O HIS D1058 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS D1068 " --> pdb=" O LYS D1064 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP D1069 " --> pdb=" O PHE D1065 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D1070 " --> pdb=" O GLN D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1098 removed outlier: 3.944A pdb=" N SER D1088 " --> pdb=" O PHE D1084 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D1095 " --> pdb=" O GLN D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1141 Processing helix chain 'D' and resid 1143 through 1165 removed outlier: 3.654A pdb=" N ALA D1157 " --> pdb=" O ASN D1153 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D1158 " --> pdb=" O LYS D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1288 through 1292 removed outlier: 4.103A pdb=" N ASP D1291 " --> pdb=" O PRO D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1398 through 1403 Processing helix chain 'D' and resid 1410 through 1419 Processing helix chain 'D' and resid 1454 through 1463 Processing helix chain 'D' and resid 1485 through 1498 removed outlier: 3.692A pdb=" N LYS D1489 " --> pdb=" O TYR D1485 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR D1490 " --> pdb=" O ALA D1486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.464A pdb=" N ILE A 171 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 205 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL A 241 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR A 207 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 243 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 242 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 128 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 264 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS A 327 " --> pdb=" O VAL A 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1275 through 1277 Processing sheet with id=AA6, first strand: chain 'A' and resid 1303 through 1305 removed outlier: 3.788A pdb=" N ARG A1310 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A1308 " --> pdb=" O ASP A1305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1347 through 1348 Processing sheet with id=AA8, first strand: chain 'A' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR A1353 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A1472 " --> pdb=" O LYS A1378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1427 through 1428 removed outlier: 3.767A pdb=" N GLY A1427 " --> pdb=" O THR A1442 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A1442 " --> pdb=" O GLY A1427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 68 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.465A pdb=" N ILE B 171 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 205 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 241 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR B 207 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR B 243 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 242 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 128 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 264 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AB4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS B 327 " --> pdb=" O VAL B 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1275 through 1277 Processing sheet with id=AB6, first strand: chain 'B' and resid 1303 through 1305 removed outlier: 3.788A pdb=" N ARG B1310 " --> pdb=" O VAL B1303 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG B1308 " --> pdb=" O ASP B1305 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1390 through 1391 removed outlier: 7.044A pdb=" N THR B1347 " --> pdb=" O VAL B1443 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B1442 " --> pdb=" O GLY B1427 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B1427 " --> pdb=" O THR B1442 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR B1353 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B1472 " --> pdb=" O LYS B1378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 68 through 72 Processing sheet with id=AC1, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.464A pdb=" N ILE C 171 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE C 205 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 241 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR C 207 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR C 243 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 242 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 128 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 264 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 313 through 316 Processing sheet with id=AC3, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS C 327 " --> pdb=" O VAL C 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 1275 through 1277 Processing sheet with id=AC5, first strand: chain 'C' and resid 1303 through 1305 removed outlier: 3.788A pdb=" N ARG C1310 " --> pdb=" O VAL C1303 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG C1308 " --> pdb=" O ASP C1305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1347 through 1348 Processing sheet with id=AC7, first strand: chain 'C' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR C1353 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C1472 " --> pdb=" O LYS C1378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1427 through 1428 removed outlier: 3.767A pdb=" N GLY C1427 " --> pdb=" O THR C1442 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C1442 " --> pdb=" O GLY C1427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.465A pdb=" N ILE D 171 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 205 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL D 241 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR D 207 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR D 243 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 242 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 128 " --> pdb=" O TYR D 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR D 264 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 313 through 316 Processing sheet with id=AD3, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.583A pdb=" N CYS D 327 " --> pdb=" O VAL D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 1275 through 1277 Processing sheet with id=AD5, first strand: chain 'D' and resid 1303 through 1305 removed outlier: 3.787A pdb=" N ARG D1310 " --> pdb=" O VAL D1303 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG D1308 " --> pdb=" O ASP D1305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1390 through 1391 removed outlier: 7.043A pdb=" N THR D1347 " --> pdb=" O VAL D1443 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D1442 " --> pdb=" O GLY D1427 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D1427 " --> pdb=" O THR D1442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1422 through 1423 removed outlier: 6.423A pdb=" N THR D1353 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D1472 " --> pdb=" O LYS D1378 " (cutoff:3.500A) 2022 hydrogen bonds defined for protein. 5910 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: 9.25 Time building geometry restraints manager: 4.86 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: 12414 1.34 - 1.46: 7980 1.46 - 1.57: 18082 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 38700 Sorted by residual: bond pdb=" CB TRP C 744 " pdb=" CG TRP C 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.54e+00 bond pdb=" CB TRP A 744 " pdb=" CG TRP A 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.54e+00 bond pdb=" CB TRP D 744 " pdb=" CG TRP D 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.54e+00 bond pdb=" CB TRP B 744 " pdb=" CG TRP B 744 " ideal model delta sigma weight residual 1.498 1.413 0.085 3.10e-02 1.04e+03 7.48e+00 bond pdb=" CB TRP D 835 " pdb=" CG TRP D 835 " ideal model delta sigma weight residual 1.498 1.417 0.081 3.10e-02 1.04e+03 6.90e+00 ... (remaining 38695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 51312 2.23 - 4.47: 1328 4.47 - 6.70: 236 6.70 - 8.94: 28 8.94 - 11.17: 8 Bond angle restraints: 52912 Sorted by residual: angle pdb=" N VAL B 73 " pdb=" CA VAL B 73 " pdb=" C VAL B 73 " ideal model delta sigma weight residual 113.10 108.15 4.95 9.70e-01 1.06e+00 2.60e+01 angle pdb=" N VAL D 73 " pdb=" CA VAL D 73 " pdb=" C VAL D 73 " ideal model delta sigma weight residual 113.10 108.16 4.94 9.70e-01 1.06e+00 2.59e+01 angle pdb=" N VAL A 73 " pdb=" CA VAL A 73 " pdb=" C VAL A 73 " ideal model delta sigma weight residual 113.10 108.18 4.92 9.70e-01 1.06e+00 2.57e+01 angle pdb=" N VAL C 73 " pdb=" CA VAL C 73 " pdb=" C VAL C 73 " ideal model delta sigma weight residual 113.10 108.18 4.92 9.70e-01 1.06e+00 2.57e+01 angle pdb=" C TYR B 682 " pdb=" N GLU B 683 " pdb=" CA GLU B 683 " ideal model delta sigma weight residual 120.28 115.36 4.92 1.44e+00 4.82e-01 1.17e+01 ... (remaining 52907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 20739 17.47 - 34.95: 1673 34.95 - 52.42: 284 52.42 - 69.89: 68 69.89 - 87.36: 24 Dihedral angle restraints: 22788 sinusoidal: 7652 harmonic: 15136 Sorted by residual: dihedral pdb=" CA ASP C 647 " pdb=" C ASP C 647 " pdb=" N CYS C 648 " pdb=" CA CYS C 648 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP A 647 " pdb=" C ASP A 647 " pdb=" N CYS A 648 " pdb=" CA CYS A 648 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP D 647 " pdb=" C ASP D 647 " pdb=" N CYS D 648 " pdb=" CA CYS D 648 " ideal model delta harmonic sigma weight residual 180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 22785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3736 0.035 - 0.070: 1621 0.070 - 0.105: 648 0.105 - 0.140: 193 0.140 - 0.176: 10 Chirality restraints: 6208 Sorted by residual: chirality pdb=" CA TYR C 682 " pdb=" N TYR C 682 " pdb=" C TYR C 682 " pdb=" CB TYR C 682 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR A 682 " pdb=" N TYR A 682 " pdb=" C TYR A 682 " pdb=" CB TYR A 682 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR D 682 " pdb=" N TYR D 682 " pdb=" C TYR D 682 " pdb=" CB TYR D 682 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 6205 not shown) Planarity restraints: 6784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 682 " 0.030 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" CG TYR D 682 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR D 682 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 682 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 682 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 682 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 682 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 682 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 682 " -0.030 2.00e-02 2.50e+03 2.43e-02 1.19e+01 pdb=" CG TYR C 682 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR C 682 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 682 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 682 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 682 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 682 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 682 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 682 " 0.030 2.00e-02 2.50e+03 2.43e-02 1.19e+01 pdb=" CG TYR A 682 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR A 682 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 682 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 682 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 682 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 682 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 682 " 0.003 2.00e-02 2.50e+03 ... (remaining 6781 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1103 2.65 - 3.21: 43460 3.21 - 3.77: 62094 3.77 - 4.34: 79218 4.34 - 4.90: 119427 Nonbonded interactions: 305302 Sorted by model distance: nonbonded pdb=" O LEU A 653 " pdb=" OG SER A 656 " model vdw 2.087 3.040 nonbonded pdb=" O LEU C 653 " pdb=" OG SER C 656 " model vdw 2.087 3.040 nonbonded pdb=" O LEU D 653 " pdb=" OG SER D 656 " model vdw 2.087 3.040 nonbonded pdb=" O LEU B 653 " pdb=" OG SER B 656 " model vdw 2.087 3.040 nonbonded pdb=" OG1 THR D1347 " pdb=" O GLY D1390 " model vdw 2.105 3.040 ... (remaining 305297 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 4.400 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: 0.040 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 41.120 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.010 0.085 38700 Z= 0.460 Angle : 0.891 11.171 52912 Z= 0.477 Chirality : 0.046 0.176 6208 Planarity : 0.005 0.041 6784 Dihedral : 13.827 87.363 12956 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 0.67 % Allowed : 12.02 % Favored : 87.31 % 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: -5.24 (0.09), residues: 5168 helix: -3.01 (0.07), residues: 2660 sheet: -3.24 (0.22), residues: 408 loop : -4.05 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 886 TYR 0.059 0.003 TYR C 682 PHE 0.017 0.003 PHE A 939 TRP 0.026 0.003 TRP A 835 HIS 0.007 0.002 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00980 (38700) covalent geometry : angle 0.89139 (52912) hydrogen bonds : bond 0.19129 ( 2022) hydrogen bonds : angle 8.56937 ( 5910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8848 (mtm) cc_final: 0.8371 (mpp) REVERT: A 619 MET cc_start: 0.8419 (ptm) cc_final: 0.8218 (ptm) REVERT: A 844 MET cc_start: 0.9166 (mmp) cc_final: 0.8928 (mmt) REVERT: A 1314 HIS cc_start: 0.7889 (t70) cc_final: 0.7498 (m170) REVERT: A 1365 ARG cc_start: 0.7423 (mtt90) cc_final: 0.7108 (ptt90) REVERT: B 158 MET cc_start: 0.9444 (mtp) cc_final: 0.9203 (mtp) REVERT: C 122 MET cc_start: 0.8848 (mtm) cc_final: 0.8370 (mpp) REVERT: C 844 MET cc_start: 0.9164 (mmp) cc_final: 0.8931 (mmt) REVERT: C 1314 HIS cc_start: 0.7883 (t70) cc_final: 0.7496 (m170) REVERT: C 1365 ARG cc_start: 0.7296 (mtt90) cc_final: 0.7022 (ptt-90) REVERT: D 122 MET cc_start: 0.8682 (mtm) cc_final: 0.8473 (mpp) REVERT: D 215 MET cc_start: 0.8638 (mtm) cc_final: 0.8374 (mpp) REVERT: D 1314 HIS cc_start: 0.7845 (t70) cc_final: 0.7515 (m170) outliers start: 23 outliers final: 12 residues processed: 215 average time/residue: 0.2119 time to fit residues: 79.4685 Evaluate side-chains 173 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 1451 ASP Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 1451 ASP Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 1451 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 30.0000 chunk 223 optimal weight: 0.0010 chunk 516 optimal weight: 0.0980 overall best weight: 2.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 537 GLN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1314 HIS ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN A1450 GLN ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 292 HIS ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN B 537 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS B 846 GLN B 953 GLN B1139 GLN B1314 HIS ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1437 ASN ** B1450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 292 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 537 GLN ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 846 GLN ** C1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN C1314 HIS ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1437 ASN ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 292 HIS ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 537 GLN ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 HIS D 846 GLN ** D1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN D1314 HIS ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1437 ASN D1450 GLN ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.068822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.049147 restraints weight = 258314.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.050581 restraints weight = 141188.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.051484 restraints weight = 98623.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.052013 restraints weight = 79611.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.052276 restraints weight = 70102.281| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38700 Z= 0.149 Angle : 0.644 6.661 52912 Z= 0.336 Chirality : 0.042 0.142 6208 Planarity : 0.005 0.042 6784 Dihedral : 5.120 40.308 5523 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.94 % Allowed : 13.68 % Favored : 85.38 % 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: -2.70 (0.11), residues: 5168 helix: -0.44 (0.09), residues: 2712 sheet: -3.08 (0.21), residues: 408 loop : -3.41 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1356 TYR 0.018 0.001 TYR B 682 PHE 0.028 0.002 PHE A1035 TRP 0.016 0.001 TRP A1063 HIS 0.007 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00315 (38700) covalent geometry : angle 0.64384 (52912) hydrogen bonds : bond 0.05781 ( 2022) hydrogen bonds : angle 5.38797 ( 5910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 MET cc_start: 0.8256 (ptm) cc_final: 0.8006 (ptm) REVERT: A 844 MET cc_start: 0.9067 (mmp) cc_final: 0.8831 (mmt) REVERT: A 1314 HIS cc_start: 0.7847 (t-90) cc_final: 0.7492 (m170) REVERT: B 122 MET cc_start: 0.8726 (mpp) cc_final: 0.8508 (mpp) REVERT: B 1125 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: C 844 MET cc_start: 0.9068 (mmp) cc_final: 0.8835 (mmt) REVERT: C 1314 HIS cc_start: 0.7845 (t-90) cc_final: 0.7492 (m170) REVERT: D 122 MET cc_start: 0.8886 (mtm) cc_final: 0.8619 (mpp) REVERT: D 1125 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: D 1314 HIS cc_start: 0.7857 (t-90) cc_final: 0.7571 (m170) outliers start: 32 outliers final: 24 residues processed: 227 average time/residue: 0.2079 time to fit residues: 82.9402 Evaluate side-chains 209 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1451 ASP Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1451 ASP Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 231 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 312 optimal weight: 1.9990 chunk 237 optimal weight: 20.0000 chunk 280 optimal weight: 0.0270 chunk 37 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 424 optimal weight: 4.9990 chunk 223 optimal weight: 0.4980 overall best weight: 1.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 446 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS A1089 HIS ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN B 446 HIS ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1450 GLN ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 446 HIS ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 HIS ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1450 GLN ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 446 HIS ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 HIS ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.068538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048354 restraints weight = 244058.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049844 restraints weight = 133950.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050786 restraints weight = 93250.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.051369 restraints weight = 74945.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051716 restraints weight = 65554.065| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38700 Z= 0.121 Angle : 0.583 9.969 52912 Z= 0.298 Chirality : 0.040 0.135 6208 Planarity : 0.004 0.039 6784 Dihedral : 4.625 21.965 5517 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.78 % Allowed : 15.26 % Favored : 82.95 % 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: -1.41 (0.12), residues: 5168 helix: 0.73 (0.10), residues: 2724 sheet: -2.59 (0.21), residues: 440 loop : -2.98 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A1365 TYR 0.014 0.001 TYR B1074 PHE 0.044 0.001 PHE A1035 TRP 0.011 0.001 TRP B 743 HIS 0.006 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00254 (38700) covalent geometry : angle 0.58310 (52912) hydrogen bonds : bond 0.04643 ( 2022) hydrogen bonds : angle 4.71152 ( 5910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8941 (mtm) cc_final: 0.8476 (mpp) REVERT: A 488 MET cc_start: 0.8478 (tpt) cc_final: 0.8149 (tpt) REVERT: A 844 MET cc_start: 0.9035 (mmp) cc_final: 0.8793 (mmt) REVERT: A 1050 TYR cc_start: 0.9255 (t80) cc_final: 0.9030 (t80) REVERT: A 1314 HIS cc_start: 0.7766 (t-90) cc_final: 0.7455 (m-70) REVERT: A 1365 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5595 (mtt180) REVERT: B 122 MET cc_start: 0.8804 (mpp) cc_final: 0.8559 (mpp) REVERT: C 122 MET cc_start: 0.8940 (mtm) cc_final: 0.8476 (mpp) REVERT: C 488 MET cc_start: 0.8474 (tpt) cc_final: 0.8146 (tpt) REVERT: C 844 MET cc_start: 0.9036 (mmp) cc_final: 0.8796 (mmt) REVERT: C 1050 TYR cc_start: 0.9254 (t80) cc_final: 0.9046 (t80) REVERT: C 1314 HIS cc_start: 0.7766 (t-90) cc_final: 0.7459 (m-70) REVERT: D 158 MET cc_start: 0.9531 (mtp) cc_final: 0.9311 (mtp) REVERT: D 1314 HIS cc_start: 0.7795 (t-90) cc_final: 0.7508 (m170) outliers start: 61 outliers final: 32 residues processed: 258 average time/residue: 0.2031 time to fit residues: 92.5240 Evaluate side-chains 232 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 180 optimal weight: 4.9990 chunk 382 optimal weight: 40.0000 chunk 64 optimal weight: 5.9990 chunk 368 optimal weight: 40.0000 chunk 140 optimal weight: 7.9990 chunk 443 optimal weight: 8.9990 chunk 204 optimal weight: 0.7980 chunk 275 optimal weight: 0.5980 chunk 350 optimal weight: 8.9990 chunk 412 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.068095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.047621 restraints weight = 249558.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.049151 restraints weight = 134171.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.050107 restraints weight = 92780.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.050694 restraints weight = 74163.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050997 restraints weight = 64865.963| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 38700 Z= 0.175 Angle : 0.609 8.849 52912 Z= 0.308 Chirality : 0.040 0.157 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.513 22.094 5511 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.69 % Allowed : 16.23 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.12), residues: 5168 helix: 0.93 (0.10), residues: 2736 sheet: -2.42 (0.21), residues: 440 loop : -2.74 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1356 TYR 0.020 0.001 TYR A 682 PHE 0.028 0.002 PHE B 813 TRP 0.017 0.001 TRP C1355 HIS 0.006 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00392 (38700) covalent geometry : angle 0.60854 (52912) hydrogen bonds : bond 0.04603 ( 2022) hydrogen bonds : angle 4.68204 ( 5910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 213 time to evaluate : 1.506 Fit side-chains REVERT: A 122 MET cc_start: 0.8938 (mtm) cc_final: 0.8443 (mpp) REVERT: A 680 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8283 (pp20) REVERT: A 844 MET cc_start: 0.9036 (mmp) cc_final: 0.8803 (mmt) REVERT: A 1050 TYR cc_start: 0.9282 (t80) cc_final: 0.9050 (t80) REVERT: A 1125 GLU cc_start: 0.8784 (tt0) cc_final: 0.8576 (tt0) REVERT: A 1314 HIS cc_start: 0.7763 (t-90) cc_final: 0.7445 (m-70) REVERT: A 1365 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.5598 (mtt180) REVERT: B 122 MET cc_start: 0.8791 (mpp) cc_final: 0.8528 (mpp) REVERT: B 680 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8137 (pp20) REVERT: B 1365 ARG cc_start: 0.6994 (mtt90) cc_final: 0.6788 (ptt90) REVERT: C 122 MET cc_start: 0.8933 (mtm) cc_final: 0.8438 (mpp) REVERT: C 844 MET cc_start: 0.9036 (mmp) cc_final: 0.8808 (mmt) REVERT: C 1050 TYR cc_start: 0.9290 (t80) cc_final: 0.9075 (t80) REVERT: C 1125 GLU cc_start: 0.8779 (tt0) cc_final: 0.8570 (tt0) REVERT: C 1314 HIS cc_start: 0.7764 (t-90) cc_final: 0.7447 (m-70) REVERT: D 680 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: D 1125 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: D 1314 HIS cc_start: 0.7788 (t-90) cc_final: 0.7491 (m170) REVERT: D 1365 ARG cc_start: 0.6835 (mtt90) cc_final: 0.6420 (ptt90) outliers start: 92 outliers final: 58 residues processed: 293 average time/residue: 0.2082 time to fit residues: 108.1194 Evaluate side-chains 266 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 867 PHE Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 867 PHE Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1377 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 88 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 371 optimal weight: 30.0000 chunk 469 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 440 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 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 = 0.3788 r_free = 0.3788 target = 0.067770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047578 restraints weight = 248690.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.049022 restraints weight = 137367.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049938 restraints weight = 96438.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050498 restraints weight = 77575.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.050847 restraints weight = 68114.334| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 38700 Z= 0.180 Angle : 0.612 7.994 52912 Z= 0.310 Chirality : 0.041 0.164 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.469 21.874 5511 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.92 % Allowed : 18.16 % Favored : 78.92 % 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: -0.90 (0.12), residues: 5168 helix: 1.04 (0.10), residues: 2748 sheet: -2.20 (0.21), residues: 440 loop : -2.65 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1356 TYR 0.018 0.001 TYR B 682 PHE 0.024 0.002 PHE B1035 TRP 0.012 0.001 TRP A1063 HIS 0.006 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00406 (38700) covalent geometry : angle 0.61207 (52912) hydrogen bonds : bond 0.04463 ( 2022) hydrogen bonds : angle 4.59327 ( 5910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 202 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8884 (mtm) cc_final: 0.8620 (mpp) REVERT: A 680 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: A 844 MET cc_start: 0.9040 (mmp) cc_final: 0.8786 (mmt) REVERT: A 1050 TYR cc_start: 0.9243 (t80) cc_final: 0.9001 (t80) REVERT: A 1314 HIS cc_start: 0.7770 (t-90) cc_final: 0.7455 (m-70) REVERT: A 1365 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5503 (mtt180) REVERT: B 122 MET cc_start: 0.8818 (mpp) cc_final: 0.8545 (mpp) REVERT: B 1158 MET cc_start: 0.8840 (mmp) cc_final: 0.8537 (mmm) REVERT: C 122 MET cc_start: 0.8879 (mtm) cc_final: 0.8616 (mpp) REVERT: C 680 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: C 844 MET cc_start: 0.9041 (mmp) cc_final: 0.8794 (mmt) REVERT: C 1050 TYR cc_start: 0.9257 (t80) cc_final: 0.9029 (t80) REVERT: C 1314 HIS cc_start: 0.7767 (t-90) cc_final: 0.7455 (m-70) REVERT: D 1125 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: D 1314 HIS cc_start: 0.7792 (t-90) cc_final: 0.7486 (m170) outliers start: 100 outliers final: 67 residues processed: 294 average time/residue: 0.2058 time to fit residues: 107.0328 Evaluate side-chains 270 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 867 PHE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 867 PHE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1377 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 234 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 365 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 224 optimal weight: 4.9990 chunk 500 optimal weight: 2.9990 chunk 445 optimal weight: 4.9990 chunk 442 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 HIS ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.067844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.047682 restraints weight = 248597.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.049139 restraints weight = 137629.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.050054 restraints weight = 96609.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.050616 restraints weight = 77699.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050903 restraints weight = 68233.083| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 38700 Z= 0.168 Angle : 0.600 7.317 52912 Z= 0.303 Chirality : 0.040 0.156 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.391 21.816 5511 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.78 % Allowed : 19.62 % Favored : 77.60 % 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: -0.67 (0.12), residues: 5168 helix: 1.24 (0.10), residues: 2724 sheet: -1.98 (0.22), residues: 440 loop : -2.55 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1356 TYR 0.017 0.001 TYR A 682 PHE 0.021 0.001 PHE B1035 TRP 0.012 0.001 TRP C1063 HIS 0.007 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00380 (38700) covalent geometry : angle 0.60012 (52912) hydrogen bonds : bond 0.04278 ( 2022) hydrogen bonds : angle 4.47457 ( 5910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 204 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8872 (mtm) cc_final: 0.8620 (mpp) REVERT: A 463 ASN cc_start: 0.9023 (t0) cc_final: 0.8806 (p0) REVERT: A 844 MET cc_start: 0.9046 (mmp) cc_final: 0.8769 (mmt) REVERT: A 1050 TYR cc_start: 0.9232 (t80) cc_final: 0.8996 (t80) REVERT: A 1314 HIS cc_start: 0.7799 (t-90) cc_final: 0.7480 (m-70) REVERT: A 1365 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5241 (mtt180) REVERT: B 122 MET cc_start: 0.8820 (mpp) cc_final: 0.8521 (mpp) REVERT: B 1158 MET cc_start: 0.8840 (mmp) cc_final: 0.8583 (mmm) REVERT: C 122 MET cc_start: 0.8873 (mtm) cc_final: 0.8621 (mpp) REVERT: C 463 ASN cc_start: 0.9017 (t0) cc_final: 0.8802 (p0) REVERT: C 844 MET cc_start: 0.9048 (mmp) cc_final: 0.8775 (mmt) REVERT: C 1050 TYR cc_start: 0.9248 (t80) cc_final: 0.9014 (t80) REVERT: C 1314 HIS cc_start: 0.7795 (t-90) cc_final: 0.7482 (m-70) REVERT: D 1125 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: D 1314 HIS cc_start: 0.7787 (t-90) cc_final: 0.7472 (m-70) REVERT: D 1351 MET cc_start: 0.7458 (mtt) cc_final: 0.7222 (mtt) outliers start: 95 outliers final: 72 residues processed: 296 average time/residue: 0.1994 time to fit residues: 105.2748 Evaluate side-chains 272 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 867 PHE Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 867 PHE Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 192 optimal weight: 0.9980 chunk 89 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 chunk 413 optimal weight: 2.9990 chunk 252 optimal weight: 40.0000 chunk 283 optimal weight: 4.9990 chunk 443 optimal weight: 3.9990 chunk 517 optimal weight: 30.0000 chunk 303 optimal weight: 0.9980 chunk 134 optimal weight: 50.0000 chunk 6 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.076633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.054606 restraints weight = 190610.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055541 restraints weight = 129493.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.056114 restraints weight = 101954.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.056483 restraints weight = 89510.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.056663 restraints weight = 83295.304| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 38700 Z= 0.132 Angle : 0.586 11.065 52912 Z= 0.293 Chirality : 0.040 0.134 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.289 21.618 5511 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.87 % Allowed : 19.65 % Favored : 77.49 % 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: -0.50 (0.12), residues: 5168 helix: 1.39 (0.10), residues: 2720 sheet: -1.83 (0.22), residues: 440 loop : -2.51 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1356 TYR 0.013 0.001 TYR A 682 PHE 0.022 0.001 PHE B1035 TRP 0.011 0.001 TRP D1063 HIS 0.007 0.001 HIS C1068 Details of bonding type rmsd covalent geometry : bond 0.00299 (38700) covalent geometry : angle 0.58643 (52912) hydrogen bonds : bond 0.04005 ( 2022) hydrogen bonds : angle 4.27785 ( 5910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 215 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 844 MET cc_start: 0.8953 (mmp) cc_final: 0.8737 (mmt) REVERT: A 1050 TYR cc_start: 0.9673 (t80) cc_final: 0.9438 (t80) REVERT: A 1314 HIS cc_start: 0.7770 (t-90) cc_final: 0.7476 (m-70) REVERT: A 1365 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.4962 (mtt180) REVERT: C 844 MET cc_start: 0.8934 (mmp) cc_final: 0.8733 (mmt) REVERT: C 1050 TYR cc_start: 0.9670 (t80) cc_final: 0.9440 (t80) REVERT: C 1314 HIS cc_start: 0.7777 (t-90) cc_final: 0.7480 (m-70) REVERT: D 271 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: D 931 MET cc_start: 0.7520 (ptm) cc_final: 0.7269 (ptp) REVERT: D 1314 HIS cc_start: 0.7726 (t-90) cc_final: 0.7444 (m-70) outliers start: 98 outliers final: 76 residues processed: 307 average time/residue: 0.1995 time to fit residues: 108.4953 Evaluate side-chains 275 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 197 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 867 PHE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 867 PHE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 73 optimal weight: 6.9990 chunk 448 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 416 optimal weight: 10.0000 chunk 464 optimal weight: 0.2980 chunk 330 optimal weight: 1.9990 chunk 410 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.068485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.048516 restraints weight = 244078.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.050026 restraints weight = 132684.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050972 restraints weight = 91857.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051554 restraints weight = 73303.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051903 restraints weight = 64001.589| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 38700 Z= 0.123 Angle : 0.589 11.852 52912 Z= 0.293 Chirality : 0.039 0.234 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.210 21.491 5511 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.37 % Allowed : 20.29 % Favored : 77.34 % 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: -0.36 (0.12), residues: 5168 helix: 1.47 (0.10), residues: 2732 sheet: -1.70 (0.22), residues: 448 loop : -2.42 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1356 TYR 0.012 0.001 TYR C 682 PHE 0.031 0.001 PHE B 813 TRP 0.022 0.001 TRP B1355 HIS 0.006 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00278 (38700) covalent geometry : angle 0.58870 (52912) hydrogen bonds : bond 0.03917 ( 2022) hydrogen bonds : angle 4.19268 ( 5910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 844 MET cc_start: 0.9002 (mmp) cc_final: 0.8718 (mmt) REVERT: A 1050 TYR cc_start: 0.9193 (t80) cc_final: 0.8946 (t80) REVERT: A 1314 HIS cc_start: 0.7790 (t-90) cc_final: 0.7453 (m-70) REVERT: A 1365 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5572 (mtt90) REVERT: C 844 MET cc_start: 0.8995 (mmp) cc_final: 0.8710 (mmt) REVERT: C 1050 TYR cc_start: 0.9199 (t80) cc_final: 0.8965 (t80) REVERT: C 1158 MET cc_start: 0.8961 (mmp) cc_final: 0.8526 (mmm) REVERT: C 1314 HIS cc_start: 0.7787 (t-90) cc_final: 0.7453 (m-70) REVERT: D 1158 MET cc_start: 0.8887 (mmm) cc_final: 0.8660 (mmp) REVERT: D 1314 HIS cc_start: 0.7739 (t-90) cc_final: 0.7440 (m-70) outliers start: 81 outliers final: 75 residues processed: 284 average time/residue: 0.1947 time to fit residues: 97.5943 Evaluate side-chains 276 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 200 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 867 PHE Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 867 PHE Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 491 optimal weight: 8.9990 chunk 464 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 417 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 400 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 465 optimal weight: 6.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.068042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.047690 restraints weight = 248919.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.049225 restraints weight = 133243.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.050179 restraints weight = 91957.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.050769 restraints weight = 73351.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.051143 restraints weight = 63881.433| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38700 Z= 0.184 Angle : 0.626 10.562 52912 Z= 0.312 Chirality : 0.040 0.170 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.298 21.987 5511 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.51 % Allowed : 20.38 % Favored : 77.11 % 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: -0.39 (0.12), residues: 5168 helix: 1.40 (0.10), residues: 2736 sheet: -1.63 (0.22), residues: 440 loop : -2.40 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1356 TYR 0.018 0.001 TYR C 682 PHE 0.035 0.002 PHE B 813 TRP 0.015 0.001 TRP B1355 HIS 0.006 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00418 (38700) covalent geometry : angle 0.62648 (52912) hydrogen bonds : bond 0.04214 ( 2022) hydrogen bonds : angle 4.37692 ( 5910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 203 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 844 MET cc_start: 0.9014 (mmp) cc_final: 0.8734 (mmt) REVERT: A 1050 TYR cc_start: 0.9204 (t80) cc_final: 0.8967 (t80) REVERT: A 1158 MET cc_start: 0.8868 (mmp) cc_final: 0.8648 (mmm) REVERT: A 1314 HIS cc_start: 0.7795 (t-90) cc_final: 0.7451 (m-70) REVERT: A 1365 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5440 (mtt180) REVERT: B 1158 MET cc_start: 0.8854 (mmp) cc_final: 0.8579 (mmm) REVERT: C 844 MET cc_start: 0.9018 (mmp) cc_final: 0.8741 (mmt) REVERT: C 1050 TYR cc_start: 0.9208 (t80) cc_final: 0.8991 (t80) REVERT: C 1158 MET cc_start: 0.8938 (mmp) cc_final: 0.8572 (mmp) REVERT: C 1314 HIS cc_start: 0.7790 (t-90) cc_final: 0.7450 (m-70) REVERT: D 1314 HIS cc_start: 0.7745 (t-90) cc_final: 0.7443 (m-70) outliers start: 86 outliers final: 75 residues processed: 286 average time/residue: 0.2023 time to fit residues: 102.1440 Evaluate side-chains 276 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 200 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 867 PHE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 867 PHE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 280 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 501 optimal weight: 40.0000 chunk 212 optimal weight: 0.9980 chunk 124 optimal weight: 40.0000 chunk 233 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 336 optimal weight: 0.0000 chunk 226 optimal weight: 40.0000 chunk 373 optimal weight: 50.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.068054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047785 restraints weight = 245171.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.049569 restraints weight = 143262.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.050026 restraints weight = 94130.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.050390 restraints weight = 78167.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.050484 restraints weight = 77628.560| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38700 Z= 0.161 Angle : 0.619 11.318 52912 Z= 0.307 Chirality : 0.040 0.152 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.262 21.732 5511 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.51 % Allowed : 20.58 % Favored : 76.90 % 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: -0.35 (0.12), residues: 5168 helix: 1.40 (0.10), residues: 2768 sheet: -1.58 (0.22), residues: 448 loop : -2.38 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1356 TYR 0.015 0.001 TYR B 682 PHE 0.034 0.001 PHE B 813 TRP 0.015 0.001 TRP B1355 HIS 0.007 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00366 (38700) covalent geometry : angle 0.61947 (52912) hydrogen bonds : bond 0.04101 ( 2022) hydrogen bonds : angle 4.29792 ( 5910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 200 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 MET cc_start: 0.9034 (mmp) cc_final: 0.8764 (mmt) REVERT: A 1050 TYR cc_start: 0.9323 (t80) cc_final: 0.9058 (t80) REVERT: A 1314 HIS cc_start: 0.7786 (t-90) cc_final: 0.7454 (m-70) REVERT: A 1365 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.5380 (mtt180) REVERT: B 1158 MET cc_start: 0.8875 (mmp) cc_final: 0.8604 (mmm) REVERT: C 844 MET cc_start: 0.9035 (mmp) cc_final: 0.8764 (mmt) REVERT: C 1050 TYR cc_start: 0.9328 (t80) cc_final: 0.9078 (t80) REVERT: C 1314 HIS cc_start: 0.7781 (t-90) cc_final: 0.7455 (m-70) REVERT: D 931 MET cc_start: 0.7465 (ttt) cc_final: 0.7188 (ttm) REVERT: D 1314 HIS cc_start: 0.7789 (t-90) cc_final: 0.7491 (m-70) outliers start: 86 outliers final: 79 residues processed: 283 average time/residue: 0.1861 time to fit residues: 93.6269 Evaluate side-chains 279 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 867 PHE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 867 PHE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 939 PHE Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 867 PHE Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1478 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 867 PHE Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 382 optimal weight: 30.0000 chunk 2 optimal weight: 0.0980 chunk 515 optimal weight: 50.0000 chunk 115 optimal weight: 8.9990 chunk 375 optimal weight: 30.0000 chunk 120 optimal weight: 40.0000 chunk 295 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 451 optimal weight: 0.6980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.068561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.048181 restraints weight = 250840.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.049751 restraints weight = 133673.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.050734 restraints weight = 91971.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.051319 restraints weight = 73271.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.051717 restraints weight = 63913.871| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38700 Z= 0.143 Angle : 0.608 11.044 52912 Z= 0.301 Chirality : 0.040 0.139 6208 Planarity : 0.004 0.038 6784 Dihedral : 4.212 21.688 5511 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.49 % Allowed : 20.47 % Favored : 77.05 % 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: -0.25 (0.12), residues: 5168 helix: 1.46 (0.10), residues: 2772 sheet: -1.51 (0.22), residues: 448 loop : -2.33 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1356 TYR 0.016 0.001 TYR D 682 PHE 0.030 0.001 PHE B 813 TRP 0.014 0.001 TRP B1355 HIS 0.007 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00326 (38700) covalent geometry : angle 0.60829 (52912) hydrogen bonds : bond 0.03957 ( 2022) hydrogen bonds : angle 4.21701 ( 5910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6700.59 seconds wall clock time: 116 minutes 38.50 seconds (6998.50 seconds total)