Starting phenix.real_space_refine on Mon Aug 25 18:02:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1c_18807/08_2025/8r1c_18807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1c_18807/08_2025/8r1c_18807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1c_18807/08_2025/8r1c_18807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1c_18807/08_2025/8r1c_18807.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1c_18807/08_2025/8r1c_18807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1c_18807/08_2025/8r1c_18807.cif" } resolution = 2.2 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= 0.007 sd= 0.081 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 141 5.16 5 C 19377 2.51 5 N 5010 2.21 5 O 5898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30426 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.56, per 1000 atoms: 0.22 Number of scatterers: 30426 At special positions: 0 Unit cell: (159.936, 152.633, 171.62, 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 141 16.00 O 5898 8.00 N 5010 7.00 C 19377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.04 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.04 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.04 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 654 " " NAG A1302 " - " ASN A 714 " " NAG A1303 " - " ASN A 798 " " NAG A1304 " - " ASN A1131 " " NAG A1305 " - " ASN A 706 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A1095 " " NAG A1308 " - " ASN A 279 " " NAG A1309 " - " ASN A1071 " " NAG A1310 " - " ASN A 231 " " NAG B1301 " - " ASN B 654 " " NAG B1302 " - " ASN B 714 " " NAG B1303 " - " ASN B 798 " " NAG B1304 " - " ASN B1131 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B 613 " " NAG B1307 " - " ASN B1095 " " NAG B1308 " - " ASN B 279 " " NAG B1309 " - " ASN B1071 " " NAG B1310 " - " ASN B 231 " " NAG C1301 " - " ASN C 654 " " NAG C1302 " - " ASN C 714 " " NAG C1303 " - " ASN C 798 " " NAG C1304 " - " ASN C1131 " " NAG C1305 " - " ASN C 706 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C1095 " " NAG C1308 " - " ASN C 279 " " NAG C1309 " - " ASN C1071 " " NAG C1310 " - " ASN C 231 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7194 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 69 sheets defined 22.9% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.669A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.649A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 845 through 853 removed outlier: 3.893A pdb=" N ALA A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.820A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.951A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.033A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.505A pdb=" N LYS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 63 through 66 removed outlier: 3.509A pdb=" N LYS F 66 " --> pdb=" O PRO F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 63 through 66' Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL B 364 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.669A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.649A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 845 through 853 removed outlier: 3.893A pdb=" N ALA B 849 " --> pdb=" O ASP B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.820A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 3.952A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.034A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 366 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.669A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 613 through 617 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.650A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 845 through 853 removed outlier: 3.893A pdb=" N ALA C 849 " --> pdb=" O ASP C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.820A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.952A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.033A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN A 58 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR A 266 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 132 removed outlier: 5.949A pdb=" N GLU A 129 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA A 160 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN A 131 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP A 139 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.204A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 701 removed outlier: 6.460A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.857A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.904A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.231A pdb=" N TRP H 36 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.988A pdb=" N ILE H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP H 101 " --> pdb=" O PHE H 111 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE H 111 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.411A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12 removed outlier: 5.877A pdb=" N THR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.595A pdb=" N GLY D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG D 40 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TRP D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.996A pdb=" N ILE D 113 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP D 101 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE D 111 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.416A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.914A pdb=" N THR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.597A pdb=" N GLY F 51 " --> pdb=" O TRP F 38 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG F 40 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP F 49 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.001A pdb=" N ILE F 113 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP F 101 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE F 111 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.436A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 12 removed outlier: 5.894A pdb=" N THR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN B 58 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR B 266 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'B' and resid 129 through 132 removed outlier: 5.950A pdb=" N GLU B 129 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA B 160 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 131 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP B 139 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.203A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.460A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.856A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.903A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN C 58 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 266 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AG3, first strand: chain 'C' and resid 129 through 132 removed outlier: 5.948A pdb=" N GLU C 129 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA C 160 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 131 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP C 139 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 321 through 325 removed outlier: 4.204A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AG8, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AH1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AH2, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.857A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.904A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 1117 through 1119 1322 hydrogen bonds defined for protein. 3486 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: 8.76 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.76 - 1.01: 2 1.01 - 1.26: 4921 1.26 - 1.50: 13997 1.50 - 1.75: 12030 1.75 - 2.00: 175 Bond restraints: 31125 Sorted by residual: bond pdb=" CG PRO F 9 " pdb=" CD PRO F 9 " ideal model delta sigma weight residual 1.503 0.759 0.744 3.40e-02 8.65e+02 4.78e+02 bond pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " ideal model delta sigma weight residual 1.503 0.894 0.609 3.40e-02 8.65e+02 3.21e+02 bond pdb=" CB PRO F 9 " pdb=" CG PRO F 9 " ideal model delta sigma weight residual 1.492 2.001 -0.509 5.00e-02 4.00e+02 1.04e+02 bond pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 1.468 1.564 -0.096 1.20e-02 6.94e+03 6.44e+01 bond pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 1.492 1.105 0.387 5.00e-02 4.00e+02 6.00e+01 ... (remaining 31120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 42348 14.77 - 29.55: 1 29.55 - 44.32: 6 44.32 - 59.09: 1 59.09 - 73.87: 1 Bond angle restraints: 42357 Sorted by residual: angle pdb=" N PRO D 9 " pdb=" CD PRO D 9 " pdb=" CG PRO D 9 " ideal model delta sigma weight residual 103.20 51.20 52.00 1.50e+00 4.44e-01 1.20e+03 angle pdb=" N PRO F 9 " pdb=" CD PRO F 9 " pdb=" CG PRO F 9 " ideal model delta sigma weight residual 103.20 62.65 40.55 1.50e+00 4.44e-01 7.31e+02 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 67.36 35.84 1.50e+00 4.44e-01 5.71e+02 angle pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 106.10 179.97 -73.87 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " pdb=" CG PRO D 9 " ideal model delta sigma weight residual 104.50 61.12 43.38 1.90e+00 2.77e-01 5.21e+02 ... (remaining 42352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 17724 22.75 - 45.50: 896 45.50 - 68.25: 160 68.25 - 91.00: 70 91.00 - 113.75: 2 Dihedral angle restraints: 18852 sinusoidal: 7632 harmonic: 11220 Sorted by residual: dihedral pdb=" N PRO F 9 " pdb=" C PRO F 9 " pdb=" CA PRO F 9 " pdb=" CB PRO F 9 " ideal model delta harmonic sigma weight residual 115.10 97.53 17.57 0 2.50e+00 1.60e-01 4.94e+01 dihedral pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " ideal model delta sinusoidal sigma weight residual 38.00 151.75 -113.75 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" N PRO D 9 " pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " pdb=" CB PRO D 9 " ideal model delta sinusoidal sigma weight residual 30.00 107.23 -77.23 1 1.50e+01 4.44e-03 3.32e+01 ... (remaining 18849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3625 0.048 - 0.096: 974 0.096 - 0.144: 276 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 4887 Sorted by residual: chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO D 9 " pdb=" N PRO D 9 " pdb=" C PRO D 9 " pdb=" CB PRO D 9 " both_signs ideal model delta sigma weight residual False 2.72 2.95 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO F 9 " pdb=" N PRO F 9 " pdb=" C PRO F 9 " pdb=" CB PRO F 9 " both_signs ideal model delta sigma weight residual False 2.72 2.89 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 4884 not shown) Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " -0.106 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO H 9 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 8 " 0.086 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO D 9 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO D 9 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 9 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS L 41 " 0.072 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO L 42 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.057 5.00e-02 4.00e+02 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 255 2.65 - 3.22: 26987 3.22 - 3.78: 46994 3.78 - 4.34: 69218 4.34 - 4.90: 110180 Nonbonded interactions: 253634 Sorted by model distance: nonbonded pdb=" OG1 THR C 596 " pdb=" O PRO C 597 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR A 596 " pdb=" O PRO A 597 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR B 596 " pdb=" O PRO B 597 " model vdw 2.094 3.040 nonbonded pdb=" O THR B 390 " pdb=" OG1 THR B 520 " model vdw 2.112 3.040 nonbonded pdb=" O THR C 390 " pdb=" OG1 THR C 520 " model vdw 2.112 3.040 ... (remaining 253629 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.050 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.008 0.744 31206 Z= 0.274 Angle : 0.879 73.867 42549 Z= 0.473 Chirality : 0.046 0.240 4887 Planarity : 0.005 0.152 5406 Dihedral : 14.579 113.749 11505 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.07 % Allowed : 10.53 % Favored : 88.39 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: 0.17 (0.13), residues: 3813 helix: 1.93 (0.20), residues: 714 sheet: 0.29 (0.15), residues: 1023 loop : -0.61 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1016 TYR 0.018 0.001 TYR C1064 PHE 0.015 0.001 PHE B 895 TRP 0.012 0.001 TRP H 36 HIS 0.007 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00783 (31125) covalent geometry : angle 0.86934 (42357) SS BOND : bond 0.00223 ( 51) SS BOND : angle 0.65487 ( 102) hydrogen bonds : bond 0.10424 ( 1292) hydrogen bonds : angle 6.39598 ( 3486) link_NAG-ASN : bond 0.00377 ( 30) link_NAG-ASN : angle 3.07928 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.094 Fit side-chains REVERT: A 1002 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7848 (mm110) REVERT: H 40 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7338 (ptt180) REVERT: F 9 PRO cc_start: 0.6117 (OUTLIER) cc_final: 0.5888 (Cg_exo) REVERT: F 101 ASP cc_start: 0.8005 (t0) cc_final: 0.7804 (t0) REVERT: F 119 MET cc_start: 0.6791 (mtt) cc_final: 0.6381 (mpp) REVERT: B 118 ASN cc_start: 0.7095 (t0) cc_final: 0.6701 (m110) REVERT: B 150 MET cc_start: 0.6046 (tmm) cc_final: 0.5602 (pp-130) REVERT: B 776 GLN cc_start: 0.8858 (tt0) cc_final: 0.8581 (tp40) REVERT: B 897 MET cc_start: 0.9325 (mtp) cc_final: 0.9092 (mtp) REVERT: B 932 GLN cc_start: 0.7847 (tt0) cc_final: 0.7640 (tt0) REVERT: B 1070 LYS cc_start: 0.8608 (mttt) cc_final: 0.8290 (mtpp) REVERT: C 150 MET cc_start: 0.6036 (tmm) cc_final: 0.5403 (pp-130) REVERT: C 742 ASP cc_start: 0.8132 (p0) cc_final: 0.7931 (p0) REVERT: C 776 GLN cc_start: 0.8888 (tt0) cc_final: 0.8672 (tp40) REVERT: C 1070 LYS cc_start: 0.8632 (mttt) cc_final: 0.8244 (mtpp) outliers start: 36 outliers final: 23 residues processed: 273 average time/residue: 0.6100 time to fit residues: 199.1501 Evaluate side-chains 249 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 9 PRO Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 40.0000 chunk 298 optimal weight: 20.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 999 GLN C 118 ASN C 561 GLN C 610 GLN C 910 GLN C 999 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.187950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115344 restraints weight = 27974.187| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.07 r_work: 0.3070 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 31206 Z= 0.156 Angle : 0.568 14.534 42549 Z= 0.300 Chirality : 0.046 0.175 4887 Planarity : 0.004 0.040 5406 Dihedral : 5.375 42.933 4806 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.73 % Allowed : 10.24 % Favored : 88.03 % 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 aren not related in a simple way. whole: 0.32 (0.13), residues: 3813 helix: 2.22 (0.20), residues: 693 sheet: 0.35 (0.15), residues: 1017 loop : -0.54 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 316 TYR 0.019 0.001 TYR A1064 PHE 0.018 0.001 PHE B 895 TRP 0.012 0.001 TRP H 36 HIS 0.007 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00349 (31125) covalent geometry : angle 0.54920 (42357) SS BOND : bond 0.00242 ( 51) SS BOND : angle 0.67582 ( 102) hydrogen bonds : bond 0.05290 ( 1292) hydrogen bonds : angle 5.72440 ( 3486) link_NAG-ASN : bond 0.00515 ( 30) link_NAG-ASN : angle 3.14905 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 1.150 Fit side-chains REVERT: A 169 SER cc_start: 0.7029 (OUTLIER) cc_final: 0.6753 (m) REVERT: A 455 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7871 (mtmm) REVERT: A 643 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7697 (mtp180) REVERT: A 1002 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7758 (mm110) REVERT: D 40 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6621 (ptt180) REVERT: E 40 GLN cc_start: 0.6410 (OUTLIER) cc_final: 0.5664 (tt0) REVERT: E 87 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.5964 (m-30) REVERT: F 119 MET cc_start: 0.7107 (mtt) cc_final: 0.6167 (mpp) REVERT: B 118 ASN cc_start: 0.6893 (t0) cc_final: 0.6518 (m110) REVERT: B 150 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5337 (pp-130) REVERT: B 332 LEU cc_start: 0.8041 (mm) cc_final: 0.7757 (mm) REVERT: B 643 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7203 (mpp-170) REVERT: B 776 GLN cc_start: 0.8982 (tt0) cc_final: 0.8479 (tp40) REVERT: B 847 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 932 GLN cc_start: 0.7858 (tt0) cc_final: 0.7604 (tt0) REVERT: B 1070 LYS cc_start: 0.8738 (mttt) cc_final: 0.8370 (mtpp) REVERT: C 150 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5282 (pp-130) REVERT: C 169 SER cc_start: 0.7050 (OUTLIER) cc_final: 0.6816 (m) REVERT: C 643 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7600 (mtp180) REVERT: C 742 ASP cc_start: 0.8225 (p0) cc_final: 0.7989 (p0) REVERT: C 1070 LYS cc_start: 0.8740 (mttt) cc_final: 0.8318 (mtpp) outliers start: 58 outliers final: 16 residues processed: 276 average time/residue: 0.6435 time to fit residues: 212.4381 Evaluate side-chains 259 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 112 optimal weight: 40.0000 chunk 21 optimal weight: 0.6980 chunk 363 optimal weight: 7.9990 chunk 352 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 910 GLN B 999 GLN C 118 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119650 restraints weight = 28022.904| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.09 r_work: 0.3085 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31206 Z= 0.126 Angle : 0.518 10.550 42549 Z= 0.273 Chirality : 0.044 0.163 4887 Planarity : 0.004 0.036 5406 Dihedral : 4.956 44.164 4779 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.79 % Allowed : 10.06 % Favored : 88.15 % 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 aren not related in a simple way. whole: 0.44 (0.13), residues: 3813 helix: 2.50 (0.20), residues: 672 sheet: 0.44 (0.16), residues: 987 loop : -0.49 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 316 TYR 0.018 0.001 TYR A1064 PHE 0.015 0.001 PHE B 895 TRP 0.011 0.001 TRP H 36 HIS 0.006 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00275 (31125) covalent geometry : angle 0.49900 (42357) SS BOND : bond 0.00195 ( 51) SS BOND : angle 0.59142 ( 102) hydrogen bonds : bond 0.04785 ( 1292) hydrogen bonds : angle 5.52396 ( 3486) link_NAG-ASN : bond 0.00471 ( 30) link_NAG-ASN : angle 3.01467 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 0.759 Fit side-chains REVERT: A 138 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6842 (mp) REVERT: A 169 SER cc_start: 0.7110 (OUTLIER) cc_final: 0.6836 (m) REVERT: A 228 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6950 (pp) REVERT: A 455 LYS cc_start: 0.8496 (mmtt) cc_final: 0.7910 (mtmm) REVERT: A 643 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7777 (mtp180) REVERT: A 1002 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7895 (mm110) REVERT: D 40 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6692 (ptt180) REVERT: E 40 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5538 (tt0) REVERT: E 87 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6161 (m-30) REVERT: F 119 MET cc_start: 0.7143 (mtt) cc_final: 0.6207 (mpp) REVERT: B 118 ASN cc_start: 0.6993 (t0) cc_final: 0.6604 (m110) REVERT: B 150 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5564 (pp-130) REVERT: B 355 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 455 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7828 (mtmt) REVERT: B 643 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7268 (mpp-170) REVERT: B 776 GLN cc_start: 0.8993 (tt0) cc_final: 0.8557 (tp40) REVERT: B 805 ASP cc_start: 0.7419 (t0) cc_final: 0.7181 (t0) REVERT: B 847 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7780 (mp) REVERT: B 932 GLN cc_start: 0.7961 (tt0) cc_final: 0.7719 (tt0) REVERT: B 1070 LYS cc_start: 0.8770 (mttt) cc_final: 0.8259 (mptt) REVERT: B 1098 HIS cc_start: 0.8778 (m90) cc_final: 0.8427 (m90) REVERT: C 150 MET cc_start: 0.6263 (tmm) cc_final: 0.5346 (pp-130) REVERT: C 169 SER cc_start: 0.7088 (OUTLIER) cc_final: 0.6873 (m) REVERT: C 332 LEU cc_start: 0.8017 (mm) cc_final: 0.7773 (mm) REVERT: C 643 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7671 (mtp180) REVERT: C 742 ASP cc_start: 0.8294 (p0) cc_final: 0.8036 (p0) REVERT: C 1070 LYS cc_start: 0.8752 (mttt) cc_final: 0.8388 (mtpp) outliers start: 60 outliers final: 21 residues processed: 288 average time/residue: 0.5834 time to fit residues: 201.6757 Evaluate side-chains 266 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 51 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 154 optimal weight: 50.0000 chunk 363 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 338 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 999 GLN C 118 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.187358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115902 restraints weight = 27956.347| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.26 r_work: 0.3055 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31206 Z= 0.182 Angle : 0.576 10.580 42549 Z= 0.305 Chirality : 0.047 0.180 4887 Planarity : 0.004 0.044 5406 Dihedral : 5.256 46.614 4779 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.64 % Allowed : 10.30 % Favored : 88.06 % 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 aren not related in a simple way. whole: 0.35 (0.13), residues: 3813 helix: 2.28 (0.20), residues: 675 sheet: 0.38 (0.16), residues: 972 loop : -0.48 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 316 TYR 0.019 0.002 TYR A1064 PHE 0.020 0.002 PHE B 895 TRP 0.011 0.001 TRP H 36 HIS 0.007 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00411 (31125) covalent geometry : angle 0.55787 (42357) SS BOND : bond 0.00292 ( 51) SS BOND : angle 0.74034 ( 102) hydrogen bonds : bond 0.05504 ( 1292) hydrogen bonds : angle 5.71645 ( 3486) link_NAG-ASN : bond 0.00515 ( 30) link_NAG-ASN : angle 3.11794 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 1.499 Fit side-chains REVERT: A 455 LYS cc_start: 0.8495 (mmtt) cc_final: 0.7895 (mtmm) REVERT: A 643 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8103 (mtp180) REVERT: D 40 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6679 (ptt180) REVERT: E 40 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5441 (tt0) REVERT: E 87 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: B 118 ASN cc_start: 0.6958 (t0) cc_final: 0.6608 (m110) REVERT: B 150 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5722 (mpt) REVERT: B 332 LEU cc_start: 0.8059 (mm) cc_final: 0.7795 (mm) REVERT: B 643 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7266 (mpp-170) REVERT: B 776 GLN cc_start: 0.9013 (tt0) cc_final: 0.8555 (tp40) REVERT: B 805 ASP cc_start: 0.7440 (t0) cc_final: 0.7149 (t0) REVERT: B 847 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7658 (mp) REVERT: B 932 GLN cc_start: 0.8021 (tt0) cc_final: 0.7748 (tt0) REVERT: B 1070 LYS cc_start: 0.8828 (mttt) cc_final: 0.8289 (mptt) REVERT: C 118 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6640 (m110) REVERT: C 138 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6878 (mp) REVERT: C 150 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5191 (pp-130) REVERT: C 332 LEU cc_start: 0.7948 (mm) cc_final: 0.7650 (mm) REVERT: C 643 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7702 (mtp180) REVERT: C 742 ASP cc_start: 0.8272 (p0) cc_final: 0.8024 (p0) REVERT: C 1070 LYS cc_start: 0.8818 (mttt) cc_final: 0.8437 (mtpp) outliers start: 55 outliers final: 24 residues processed: 273 average time/residue: 0.6469 time to fit residues: 211.0416 Evaluate side-chains 264 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 276 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 113 optimal weight: 40.0000 chunk 171 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 337 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 348 optimal weight: 0.4980 chunk 187 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.188363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115624 restraints weight = 27925.923| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.18 r_work: 0.3077 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31206 Z= 0.128 Angle : 0.524 10.272 42549 Z= 0.276 Chirality : 0.045 0.164 4887 Planarity : 0.003 0.035 5406 Dihedral : 5.024 46.801 4779 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.40 % Allowed : 11.01 % Favored : 87.59 % 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 aren not related in a simple way. whole: 0.41 (0.13), residues: 3813 helix: 2.41 (0.20), residues: 675 sheet: 0.39 (0.16), residues: 978 loop : -0.46 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 316 TYR 0.018 0.001 TYR A1064 PHE 0.015 0.001 PHE B 895 TRP 0.012 0.001 TRP F 36 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00279 (31125) covalent geometry : angle 0.50535 (42357) SS BOND : bond 0.00197 ( 51) SS BOND : angle 0.59866 ( 102) hydrogen bonds : bond 0.04817 ( 1292) hydrogen bonds : angle 5.52634 ( 3486) link_NAG-ASN : bond 0.00463 ( 30) link_NAG-ASN : angle 3.00438 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 1.240 Fit side-chains REVERT: A 316 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.7153 (mpt90) REVERT: A 455 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7838 (mtmm) REVERT: A 643 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: A 1002 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7736 (mm110) REVERT: L 40 GLN cc_start: 0.6457 (OUTLIER) cc_final: 0.4557 (tp40) REVERT: E 40 GLN cc_start: 0.6177 (OUTLIER) cc_final: 0.5304 (tt0) REVERT: E 87 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6049 (m-30) REVERT: B 118 ASN cc_start: 0.6863 (t0) cc_final: 0.6515 (m110) REVERT: B 150 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5748 (mpt) REVERT: B 332 LEU cc_start: 0.7954 (mm) cc_final: 0.7709 (mm) REVERT: B 455 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7784 (mtmt) REVERT: B 643 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7225 (mpp-170) REVERT: B 776 GLN cc_start: 0.8986 (tt0) cc_final: 0.8419 (tp40) REVERT: B 805 ASP cc_start: 0.7273 (t0) cc_final: 0.6969 (t0) REVERT: B 932 GLN cc_start: 0.7917 (tt0) cc_final: 0.7632 (tt0) REVERT: B 961 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7912 (mppt) REVERT: B 1070 LYS cc_start: 0.8745 (mttt) cc_final: 0.8148 (mptt) REVERT: C 118 ASN cc_start: 0.6905 (t0) cc_final: 0.6584 (m110) REVERT: C 138 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6790 (mp) REVERT: C 150 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5190 (pp-130) REVERT: C 169 SER cc_start: 0.7059 (OUTLIER) cc_final: 0.6838 (m) REVERT: C 318 GLN cc_start: 0.8256 (mm110) cc_final: 0.8033 (mm110) REVERT: C 332 LEU cc_start: 0.7885 (mm) cc_final: 0.7530 (mm) REVERT: C 437 LYS cc_start: 0.8173 (mttt) cc_final: 0.7914 (mtpt) REVERT: C 643 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7576 (mtp180) REVERT: C 742 ASP cc_start: 0.8224 (p0) cc_final: 0.7968 (p0) REVERT: C 776 GLN cc_start: 0.8974 (tt0) cc_final: 0.8515 (tp40) REVERT: C 1070 LYS cc_start: 0.8732 (mttt) cc_final: 0.8304 (mtpp) outliers start: 47 outliers final: 20 residues processed: 268 average time/residue: 0.6591 time to fit residues: 210.6239 Evaluate side-chains 268 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 229 optimal weight: 6.9990 chunk 316 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 380 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 121 optimal weight: 40.0000 chunk 206 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 118 ASN C 561 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.187771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115341 restraints weight = 27873.803| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.12 r_work: 0.3063 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31206 Z= 0.151 Angle : 0.544 10.203 42549 Z= 0.287 Chirality : 0.045 0.168 4887 Planarity : 0.004 0.037 5406 Dihedral : 5.117 47.725 4779 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.61 % Allowed : 11.04 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.13), residues: 3813 helix: 2.20 (0.20), residues: 693 sheet: 0.41 (0.16), residues: 975 loop : -0.46 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1036 TYR 0.019 0.001 TYR A1064 PHE 0.017 0.001 PHE B 895 TRP 0.011 0.001 TRP H 36 HIS 0.006 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00335 (31125) covalent geometry : angle 0.52608 (42357) SS BOND : bond 0.00239 ( 51) SS BOND : angle 0.65869 ( 102) hydrogen bonds : bond 0.05126 ( 1292) hydrogen bonds : angle 5.58795 ( 3486) link_NAG-ASN : bond 0.00473 ( 30) link_NAG-ASN : angle 3.01253 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 1.043 Fit side-chains REVERT: A 437 LYS cc_start: 0.8279 (mttt) cc_final: 0.7990 (mtpt) REVERT: A 455 LYS cc_start: 0.8469 (mmtt) cc_final: 0.7859 (mtmm) REVERT: A 643 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7677 (mtp180) REVERT: A 961 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7990 (mppt) REVERT: A 1002 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7760 (mm110) REVERT: A 1098 HIS cc_start: 0.8714 (m90) cc_final: 0.8464 (m90) REVERT: L 40 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.4602 (tp40) REVERT: D 40 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6642 (ptt180) REVERT: E 28 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7573 (p0) REVERT: E 40 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.5262 (tt0) REVERT: E 87 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6054 (m-30) REVERT: G 49 MET cc_start: 0.7147 (mmp) cc_final: 0.6935 (mmp) REVERT: B 118 ASN cc_start: 0.6931 (t0) cc_final: 0.6577 (m110) REVERT: B 150 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5723 (mpt) REVERT: B 332 LEU cc_start: 0.8024 (mm) cc_final: 0.7781 (mm) REVERT: B 437 LYS cc_start: 0.8189 (mttt) cc_final: 0.7921 (mtpt) REVERT: B 643 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7161 (mpp-170) REVERT: B 776 GLN cc_start: 0.8994 (tt0) cc_final: 0.8453 (tp40) REVERT: B 932 GLN cc_start: 0.7958 (tt0) cc_final: 0.7668 (tt0) REVERT: B 961 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7939 (mppt) REVERT: B 1070 LYS cc_start: 0.8756 (mttt) cc_final: 0.8174 (mptt) REVERT: C 118 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6625 (m110) REVERT: C 138 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6744 (mp) REVERT: C 150 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5194 (pp-130) REVERT: C 169 SER cc_start: 0.7069 (OUTLIER) cc_final: 0.6863 (m) REVERT: C 332 LEU cc_start: 0.7888 (mm) cc_final: 0.7533 (mm) REVERT: C 643 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7601 (mtp180) REVERT: C 742 ASP cc_start: 0.8233 (p0) cc_final: 0.7979 (p0) REVERT: C 1070 LYS cc_start: 0.8749 (mttt) cc_final: 0.8332 (mtpp) outliers start: 54 outliers final: 24 residues processed: 278 average time/residue: 0.6224 time to fit residues: 206.7162 Evaluate side-chains 272 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 120 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 33 optimal weight: 0.8980 chunk 271 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 121 optimal weight: 50.0000 chunk 330 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.188079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115839 restraints weight = 27866.090| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.15 r_work: 0.3062 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31206 Z= 0.137 Angle : 0.532 10.063 42549 Z= 0.280 Chirality : 0.045 0.163 4887 Planarity : 0.004 0.035 5406 Dihedral : 5.052 47.963 4779 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.61 % Allowed : 11.25 % Favored : 87.14 % 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 aren not related in a simple way. whole: 0.41 (0.13), residues: 3813 helix: 2.25 (0.20), residues: 693 sheet: 0.43 (0.16), residues: 975 loop : -0.44 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 316 TYR 0.018 0.001 TYR A1064 PHE 0.016 0.001 PHE B 895 TRP 0.011 0.001 TRP F 36 HIS 0.006 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00301 (31125) covalent geometry : angle 0.51394 (42357) SS BOND : bond 0.00212 ( 51) SS BOND : angle 0.61692 ( 102) hydrogen bonds : bond 0.04923 ( 1292) hydrogen bonds : angle 5.52940 ( 3486) link_NAG-ASN : bond 0.00456 ( 30) link_NAG-ASN : angle 2.97072 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 1.342 Fit side-chains REVERT: A 316 ARG cc_start: 0.7512 (mtt-85) cc_final: 0.7203 (mpt90) REVERT: A 437 LYS cc_start: 0.8244 (mttt) cc_final: 0.7954 (mtpt) REVERT: A 455 LYS cc_start: 0.8476 (mmtt) cc_final: 0.7861 (mtmm) REVERT: A 643 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7669 (mtp180) REVERT: A 961 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7990 (mppt) REVERT: A 1002 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7758 (mm110) REVERT: A 1098 HIS cc_start: 0.8708 (m90) cc_final: 0.8478 (m90) REVERT: L 40 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.4612 (tp40) REVERT: D 40 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6604 (ptt180) REVERT: E 40 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5253 (tt0) REVERT: E 87 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6076 (m-30) REVERT: B 118 ASN cc_start: 0.6944 (t0) cc_final: 0.6586 (m110) REVERT: B 150 MET cc_start: 0.6183 (OUTLIER) cc_final: 0.5740 (mpt) REVERT: B 332 LEU cc_start: 0.8006 (mm) cc_final: 0.7768 (mm) REVERT: B 355 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 437 LYS cc_start: 0.8176 (mttt) cc_final: 0.7903 (mtpt) REVERT: B 643 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7192 (mpp-170) REVERT: B 776 GLN cc_start: 0.9003 (tt0) cc_final: 0.8440 (tp40) REVERT: B 847 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7607 (mp) REVERT: B 932 GLN cc_start: 0.7930 (tt0) cc_final: 0.7638 (tt0) REVERT: B 961 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7928 (mppt) REVERT: B 1070 LYS cc_start: 0.8757 (mttt) cc_final: 0.8171 (mptt) REVERT: C 138 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6806 (mp) REVERT: C 150 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5272 (pp-130) REVERT: C 318 GLN cc_start: 0.8261 (mm110) cc_final: 0.8061 (mm110) REVERT: C 332 LEU cc_start: 0.7850 (mm) cc_final: 0.7487 (mm) REVERT: C 643 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7599 (mtp180) REVERT: C 742 ASP cc_start: 0.8222 (p0) cc_final: 0.7968 (p0) REVERT: C 1070 LYS cc_start: 0.8749 (mttt) cc_final: 0.8326 (mtpp) outliers start: 54 outliers final: 24 residues processed: 273 average time/residue: 0.6209 time to fit residues: 201.9372 Evaluate side-chains 268 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 264 optimal weight: 5.9990 chunk 109 optimal weight: 50.0000 chunk 203 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 359 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 147 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 610 GLN A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 999 GLN C 23 GLN C 122 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.186409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112886 restraints weight = 27863.933| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.09 r_work: 0.3042 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31206 Z= 0.232 Angle : 0.620 10.085 42549 Z= 0.330 Chirality : 0.049 0.209 4887 Planarity : 0.004 0.052 5406 Dihedral : 5.515 49.945 4779 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.55 % Allowed : 11.19 % Favored : 87.26 % 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 aren not related in a simple way. whole: 0.21 (0.13), residues: 3813 helix: 2.01 (0.20), residues: 693 sheet: 0.27 (0.15), residues: 1005 loop : -0.54 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 316 TYR 0.022 0.002 TYR A 753 PHE 0.022 0.002 PHE B 895 TRP 0.011 0.002 TRP H 36 HIS 0.008 0.002 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00531 (31125) covalent geometry : angle 0.60270 (42357) SS BOND : bond 0.00371 ( 51) SS BOND : angle 0.88365 ( 102) hydrogen bonds : bond 0.05919 ( 1292) hydrogen bonds : angle 5.81792 ( 3486) link_NAG-ASN : bond 0.00548 ( 30) link_NAG-ASN : angle 3.11114 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.902 Fit side-chains REVERT: A 437 LYS cc_start: 0.8288 (mttt) cc_final: 0.8001 (mtpt) REVERT: A 455 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7902 (mtmm) REVERT: A 643 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7988 (mtp180) REVERT: A 961 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8219 (mtpt) REVERT: A 1002 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7684 (mm110) REVERT: D 40 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6663 (ptt180) REVERT: E 40 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.5353 (tt0) REVERT: E 87 ASP cc_start: 0.6649 (OUTLIER) cc_final: 0.6015 (m-30) REVERT: B 118 ASN cc_start: 0.6937 (t0) cc_final: 0.6647 (m110) REVERT: B 150 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5551 (mpt) REVERT: B 318 GLN cc_start: 0.8127 (mm110) cc_final: 0.7913 (mm110) REVERT: B 437 LYS cc_start: 0.8182 (mttt) cc_final: 0.7897 (mtpt) REVERT: B 643 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7171 (mpp-170) REVERT: B 776 GLN cc_start: 0.8975 (tt0) cc_final: 0.8418 (tp40) REVERT: B 847 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7595 (mp) REVERT: B 932 GLN cc_start: 0.7942 (tt0) cc_final: 0.7639 (tt0) REVERT: B 961 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7904 (mppt) REVERT: B 1070 LYS cc_start: 0.8766 (mttt) cc_final: 0.8172 (mptt) REVERT: C 118 ASN cc_start: 0.6974 (t0) cc_final: 0.6664 (m110) REVERT: C 138 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6793 (mp) REVERT: C 150 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5274 (pp-130) REVERT: C 332 LEU cc_start: 0.7891 (mm) cc_final: 0.7541 (mm) REVERT: C 437 LYS cc_start: 0.8219 (mttt) cc_final: 0.7965 (mtpt) REVERT: C 643 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: C 742 ASP cc_start: 0.8214 (p0) cc_final: 0.7952 (p0) REVERT: C 932 GLN cc_start: 0.8001 (tt0) cc_final: 0.7742 (tt0) REVERT: C 1070 LYS cc_start: 0.8737 (mttt) cc_final: 0.8322 (mtpp) outliers start: 52 outliers final: 27 residues processed: 266 average time/residue: 0.5584 time to fit residues: 176.9597 Evaluate side-chains 264 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 302 optimal weight: 0.8980 chunk 181 optimal weight: 30.0000 chunk 253 optimal weight: 0.8980 chunk 346 optimal weight: 0.8980 chunk 319 optimal weight: 9.9990 chunk 308 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.188701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116675 restraints weight = 27905.583| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.23 r_work: 0.3082 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 31206 Z= 0.111 Angle : 0.514 9.947 42549 Z= 0.269 Chirality : 0.044 0.154 4887 Planarity : 0.003 0.035 5406 Dihedral : 4.994 49.089 4779 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.31 % Allowed : 11.70 % Favored : 86.99 % 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 aren not related in a simple way. whole: 0.44 (0.13), residues: 3813 helix: 2.32 (0.20), residues: 693 sheet: 0.46 (0.16), residues: 969 loop : -0.46 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 316 TYR 0.016 0.001 TYR A1064 PHE 0.015 0.001 PHE C 562 TRP 0.013 0.001 TRP H 36 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00233 (31125) covalent geometry : angle 0.49585 (42357) SS BOND : bond 0.00166 ( 51) SS BOND : angle 0.57893 ( 102) hydrogen bonds : bond 0.04521 ( 1292) hydrogen bonds : angle 5.44737 ( 3486) link_NAG-ASN : bond 0.00429 ( 30) link_NAG-ASN : angle 2.92980 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 1.226 Fit side-chains REVERT: A 316 ARG cc_start: 0.7468 (mtt-85) cc_final: 0.7207 (mpt90) REVERT: A 437 LYS cc_start: 0.8251 (mttt) cc_final: 0.7963 (mtpt) REVERT: A 455 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7863 (mtmm) REVERT: A 643 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7661 (mtp180) REVERT: A 1002 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7744 (mm110) REVERT: A 1098 HIS cc_start: 0.8682 (m90) cc_final: 0.8452 (m90) REVERT: L 40 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.4238 (tp40) REVERT: D 40 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6591 (ptt180) REVERT: E 40 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5163 (tt0) REVERT: E 87 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6055 (m-30) REVERT: B 150 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5767 (mpt) REVERT: B 318 GLN cc_start: 0.8172 (mm110) cc_final: 0.7945 (mm110) REVERT: B 332 LEU cc_start: 0.7993 (mm) cc_final: 0.7742 (mm) REVERT: B 437 LYS cc_start: 0.8136 (mttt) cc_final: 0.7861 (mtpt) REVERT: B 643 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7171 (mpp-170) REVERT: B 776 GLN cc_start: 0.8975 (tt0) cc_final: 0.8398 (tp40) REVERT: B 932 GLN cc_start: 0.7939 (tt0) cc_final: 0.7650 (tt0) REVERT: B 961 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7905 (mppt) REVERT: B 1070 LYS cc_start: 0.8743 (mttt) cc_final: 0.8149 (mptt) REVERT: B 1089 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7855 (pp20) REVERT: C 138 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6832 (mp) REVERT: C 150 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5246 (pp-130) REVERT: C 332 LEU cc_start: 0.7820 (mm) cc_final: 0.7454 (mm) REVERT: C 437 LYS cc_start: 0.8176 (mttt) cc_final: 0.7933 (mtpt) REVERT: C 643 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7582 (mtp180) REVERT: C 742 ASP cc_start: 0.8204 (p0) cc_final: 0.7942 (p0) REVERT: C 1070 LYS cc_start: 0.8732 (mttt) cc_final: 0.8302 (mtpp) outliers start: 44 outliers final: 24 residues processed: 266 average time/residue: 0.5738 time to fit residues: 182.1009 Evaluate side-chains 262 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 938 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 144 optimal weight: 8.9990 chunk 143 optimal weight: 40.0000 chunk 264 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 304 optimal weight: 0.0970 chunk 339 optimal weight: 0.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.188074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115805 restraints weight = 27765.948| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.15 r_work: 0.3070 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31206 Z= 0.133 Angle : 0.532 10.279 42549 Z= 0.279 Chirality : 0.045 0.159 4887 Planarity : 0.004 0.035 5406 Dihedral : 5.044 49.210 4779 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.25 % Allowed : 11.82 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.13), residues: 3813 helix: 2.29 (0.20), residues: 693 sheet: 0.44 (0.16), residues: 975 loop : -0.44 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 316 TYR 0.018 0.001 TYR A1064 PHE 0.016 0.001 PHE B 895 TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00291 (31125) covalent geometry : angle 0.51470 (42357) SS BOND : bond 0.00207 ( 51) SS BOND : angle 0.61280 ( 102) hydrogen bonds : bond 0.04874 ( 1292) hydrogen bonds : angle 5.50554 ( 3486) link_NAG-ASN : bond 0.00443 ( 30) link_NAG-ASN : angle 2.94022 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 1.211 Fit side-chains REVERT: A 316 ARG cc_start: 0.7467 (mtt-85) cc_final: 0.7207 (mpt90) REVERT: A 437 LYS cc_start: 0.8235 (mttt) cc_final: 0.7971 (mtpt) REVERT: A 455 LYS cc_start: 0.8483 (mmtt) cc_final: 0.7860 (mtmm) REVERT: A 490 ARG cc_start: 0.7255 (mmt90) cc_final: 0.6951 (tpp-160) REVERT: A 643 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7667 (mtp180) REVERT: A 961 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7969 (mppt) REVERT: A 1002 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7747 (mm110) REVERT: A 1098 HIS cc_start: 0.8704 (m90) cc_final: 0.8476 (m90) REVERT: L 40 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.4298 (tp40) REVERT: D 40 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6622 (ptt180) REVERT: E 40 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5162 (tt0) REVERT: E 87 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6089 (m-30) REVERT: B 150 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5798 (mpt) REVERT: B 332 LEU cc_start: 0.8021 (mm) cc_final: 0.7773 (mm) REVERT: B 437 LYS cc_start: 0.8140 (mttt) cc_final: 0.7870 (mtpt) REVERT: B 643 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7182 (mpp-170) REVERT: B 776 GLN cc_start: 0.8983 (tt0) cc_final: 0.8420 (tp40) REVERT: B 932 GLN cc_start: 0.7971 (tt0) cc_final: 0.7678 (tt0) REVERT: B 961 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7894 (mppt) REVERT: B 1070 LYS cc_start: 0.8753 (mttt) cc_final: 0.8163 (mptt) REVERT: B 1089 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7850 (pp20) REVERT: C 138 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6865 (mp) REVERT: C 150 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5293 (pp-130) REVERT: C 332 LEU cc_start: 0.7809 (mm) cc_final: 0.7437 (mm) REVERT: C 437 LYS cc_start: 0.8182 (mttt) cc_final: 0.7947 (mtpt) REVERT: C 643 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7577 (mtp180) REVERT: C 742 ASP cc_start: 0.8205 (p0) cc_final: 0.7953 (p0) REVERT: C 1070 LYS cc_start: 0.8744 (mttt) cc_final: 0.8324 (mtpp) outliers start: 42 outliers final: 26 residues processed: 263 average time/residue: 0.6793 time to fit residues: 211.9783 Evaluate side-chains 267 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 938 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 137 optimal weight: 40.0000 chunk 206 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 chunk 179 optimal weight: 40.0000 chunk 318 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 625 GLN C 999 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113568 restraints weight = 27915.394| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.04 r_work: 0.3058 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31206 Z= 0.194 Angle : 0.589 10.676 42549 Z= 0.312 Chirality : 0.047 0.182 4887 Planarity : 0.004 0.045 5406 Dihedral : 5.376 50.591 4779 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.34 % Allowed : 11.73 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.13), residues: 3813 helix: 2.10 (0.20), residues: 693 sheet: 0.40 (0.16), residues: 975 loop : -0.52 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 316 TYR 0.019 0.002 TYR A1064 PHE 0.019 0.002 PHE B 895 TRP 0.010 0.002 TRP H 36 HIS 0.007 0.001 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00440 (31125) covalent geometry : angle 0.57280 (42357) SS BOND : bond 0.00313 ( 51) SS BOND : angle 0.78438 ( 102) hydrogen bonds : bond 0.05587 ( 1292) hydrogen bonds : angle 5.71209 ( 3486) link_NAG-ASN : bond 0.00500 ( 30) link_NAG-ASN : angle 3.02510 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18244.40 seconds wall clock time: 309 minutes 26.20 seconds (18566.20 seconds total)