Starting phenix.real_space_refine on Mon Sep 14 14:22:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.map" model { file = "/net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bcq_7085/09_2026/6bcq_7085.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 19944 2.51 5 N 5432 2.21 5 O 5520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31048 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7731 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 38, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, C, D Time building chain proxies: 10.51, per 1000 atoms: 0.34 Number of scatterers: 31048 At special positions: 0 Unit cell: (153.01, 153.01, 178.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 12 15.00 O 5520 8.00 N 5432 7.00 C 19944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.04 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.04 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.04 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7344 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 12 sheets defined 67.3% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 14 through 20 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.850A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 162 through 177 removed outlier: 4.336A pdb=" N HIS B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.525A pdb=" N MET B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.700A pdb=" N GLN B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 Processing helix chain 'B' and resid 305 through 316 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.945A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 385 removed outlier: 3.947A pdb=" N THR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 404 Processing helix chain 'B' and resid 406 through 415 removed outlier: 3.858A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.737A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 472 through 482 removed outlier: 4.031A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.515A pdb=" N SER B 588 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.714A pdb=" N SER B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.684A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 682 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.525A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 removed outlier: 3.823A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 774 through 799 removed outlier: 3.633A pdb=" N ALA B 778 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 830 Processing helix chain 'B' and resid 849 through 857 Processing helix chain 'B' and resid 859 through 879 removed outlier: 3.814A pdb=" N LEU B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 901 removed outlier: 4.262A pdb=" N MET B 896 " --> pdb=" O CYS B 892 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 removed outlier: 3.731A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 909 No H-bonds generated for 'chain 'B' and resid 907 through 909' Processing helix chain 'B' and resid 912 through 920 removed outlier: 4.271A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 Processing helix chain 'B' and resid 954 through 964 Processing helix chain 'B' and resid 964 through 969 Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1013 through 1029 Processing helix chain 'B' and resid 1029 through 1067 removed outlier: 5.273A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1090 removed outlier: 3.894A pdb=" N ARG B1090 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1141 Processing helix chain 'B' and resid 1142 through 1192 removed outlier: 3.676A pdb=" N GLN B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B1166 " --> pdb=" O GLY B1162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B1168 " --> pdb=" O ILE B1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS B1181 " --> pdb=" O GLU B1177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B1184 " --> pdb=" O HIS B1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 20 Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.850A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 162 through 177 removed outlier: 4.337A pdb=" N HIS A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.525A pdb=" N MET A 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.700A pdb=" N GLN A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 344 through 359 removed outlier: 3.945A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 removed outlier: 3.946A pdb=" N THR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.858A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.737A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 472 through 482 removed outlier: 4.031A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.514A pdb=" N SER A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 removed outlier: 3.715A pdb=" N SER A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.684A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.526A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 703 removed outlier: 3.823A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 774 through 799 removed outlier: 3.634A pdb=" N ALA A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 830 Processing helix chain 'A' and resid 849 through 857 Processing helix chain 'A' and resid 859 through 879 removed outlier: 3.813A pdb=" N LEU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 901 removed outlier: 4.263A pdb=" N MET A 896 " --> pdb=" O CYS A 892 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.731A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.271A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1013 through 1029 Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.272A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1090 removed outlier: 3.894A pdb=" N ARG A1090 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1141 Processing helix chain 'A' and resid 1142 through 1192 removed outlier: 3.676A pdb=" N GLN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A1168 " --> pdb=" O ILE A1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A1181 " --> pdb=" O GLU A1177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A1184 " --> pdb=" O HIS A1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 20 Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.850A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 162 through 177 removed outlier: 4.337A pdb=" N HIS C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.526A pdb=" N MET C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.699A pdb=" N GLN C 261 " --> pdb=" O TYR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 305 through 316 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 344 through 359 removed outlier: 3.945A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 385 removed outlier: 3.947A pdb=" N THR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 404 Processing helix chain 'C' and resid 406 through 415 removed outlier: 3.858A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 415 " --> pdb=" O GLN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.737A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 447 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 472 through 482 removed outlier: 4.030A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.515A pdb=" N SER C 588 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 removed outlier: 3.714A pdb=" N SER C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 643 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.684A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 682 Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.525A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS C 699 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 703 removed outlier: 3.823A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 774 through 799 removed outlier: 3.633A pdb=" N ALA C 778 " --> pdb=" O ALA C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 830 Processing helix chain 'C' and resid 849 through 857 Processing helix chain 'C' and resid 859 through 879 removed outlier: 3.813A pdb=" N LEU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 901 removed outlier: 4.262A pdb=" N MET C 896 " --> pdb=" O CYS C 892 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 897 " --> pdb=" O LEU C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.732A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 912 through 920 removed outlier: 4.270A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 Processing helix chain 'C' and resid 954 through 964 Processing helix chain 'C' and resid 964 through 969 Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1013 through 1029 Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.272A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1090 removed outlier: 3.892A pdb=" N ARG C1090 " --> pdb=" O LYS C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1141 Processing helix chain 'C' and resid 1142 through 1192 removed outlier: 3.675A pdb=" N GLN C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C1164 " --> pdb=" O GLN C1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C1166 " --> pdb=" O GLY C1162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C1168 " --> pdb=" O ILE C1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C1169 " --> pdb=" O ARG C1165 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS C1181 " --> pdb=" O GLU C1177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C1184 " --> pdb=" O HIS C1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 20 Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.851A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 143 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 162 through 177 removed outlier: 4.336A pdb=" N HIS D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.526A pdb=" N MET D 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.699A pdb=" N GLN D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 305 through 316 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 344 through 359 removed outlier: 3.945A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 385 removed outlier: 3.946A pdb=" N THR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 404 Processing helix chain 'D' and resid 406 through 415 removed outlier: 3.857A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.737A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER D 429 " --> pdb=" O HIS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 447 Processing helix chain 'D' and resid 457 through 465 Processing helix chain 'D' and resid 472 through 482 removed outlier: 4.030A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.515A pdb=" N SER D 588 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.715A pdb=" N SER D 634 " --> pdb=" O CYS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 removed outlier: 3.684A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 682 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.525A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS D 699 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 703 removed outlier: 3.824A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 700 through 703' Processing helix chain 'D' and resid 774 through 799 removed outlier: 3.633A pdb=" N ALA D 778 " --> pdb=" O ALA D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 830 Processing helix chain 'D' and resid 849 through 857 Processing helix chain 'D' and resid 859 through 879 removed outlier: 3.813A pdb=" N LEU D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 901 removed outlier: 4.263A pdb=" N MET D 896 " --> pdb=" O CYS D 892 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 897 " --> pdb=" O LEU D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 removed outlier: 3.732A pdb=" N PHE D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 909 No H-bonds generated for 'chain 'D' and resid 907 through 909' Processing helix chain 'D' and resid 912 through 920 removed outlier: 4.271A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 Processing helix chain 'D' and resid 954 through 964 Processing helix chain 'D' and resid 964 through 969 Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1013 through 1029 Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.273A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1090 removed outlier: 3.892A pdb=" N ARG D1090 " --> pdb=" O LYS D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1141 Processing helix chain 'D' and resid 1142 through 1192 removed outlier: 3.676A pdb=" N GLN D1163 " --> pdb=" O LYS D1159 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D1166 " --> pdb=" O GLY D1162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D1168 " --> pdb=" O ILE D1164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG D1169 " --> pdb=" O ARG D1165 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS D1181 " --> pdb=" O GLU D1177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D1184 " --> pdb=" O HIS D1180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 211 through 212 removed outlier: 7.960A pdb=" N TYR B 212 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 80 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN B 90 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU B 235 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU B 92 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP B 237 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 94 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE B 154 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 189 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 156 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 119 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 277 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER B 121 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 986 removed outlier: 4.205A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 212 removed outlier: 7.959A pdb=" N TYR A 212 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 80 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN A 90 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU A 235 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU A 92 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP A 237 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 94 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE A 154 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 189 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 156 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL A 119 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU A 277 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 121 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 986 removed outlier: 4.205A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 211 through 212 removed outlier: 7.960A pdb=" N TYR C 212 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP C 80 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN C 90 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU C 235 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU C 92 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP C 237 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU C 94 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE C 154 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 189 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 156 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 119 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU C 277 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER C 121 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 986 removed outlier: 4.204A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 211 through 212 removed outlier: 7.959A pdb=" N TYR D 212 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP D 80 " --> pdb=" O TYR D 212 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN D 90 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU D 235 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D 92 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP D 237 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU D 94 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE D 154 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 189 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 156 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL D 119 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 277 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER D 121 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 986 removed outlier: 4.205A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) 1824 hydrogen bonds defined for protein. 5412 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: 6.85 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9953 1.34 - 1.46: 6167 1.46 - 1.58: 15396 1.58 - 1.69: 20 1.69 - 1.81: 208 Bond restraints: 31744 Sorted by residual: bond pdb=" C4 ATP D2000 " pdb=" C5 ATP D2000 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C4 ATP C2000 " pdb=" C5 ATP C2000 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.63e+01 bond pdb=" C5 ATP B2000 " pdb=" C6 ATP B2000 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 ... (remaining 31739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 42734 3.99 - 7.98: 314 7.98 - 11.98: 28 11.98 - 15.97: 4 15.97 - 19.96: 4 Bond angle restraints: 43084 Sorted by residual: angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 119.91 19.96 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PB ATP D2000 " pdb=" O3B ATP D2000 " pdb=" PG ATP D2000 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 angle pdb=" PA ATP D2000 " pdb=" O3A ATP D2000 " pdb=" PB ATP D2000 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 ... (remaining 43079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 17977 15.74 - 31.48: 607 31.48 - 47.22: 140 47.22 - 62.96: 16 62.96 - 78.71: 28 Dihedral angle restraints: 18768 sinusoidal: 7420 harmonic: 11348 Sorted by residual: dihedral pdb=" CA ILE A 279 " pdb=" C ILE A 279 " pdb=" N ASP A 280 " pdb=" CA ASP A 280 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ILE C 279 " pdb=" C ILE C 279 " pdb=" N ASP C 280 " pdb=" CA ASP C 280 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ILE D 279 " pdb=" C ILE D 279 " pdb=" N ASP D 280 " pdb=" CA ASP D 280 " ideal model delta harmonic sigma weight residual -180.00 -153.83 -26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 18765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3699 0.057 - 0.113: 1044 0.113 - 0.170: 109 0.170 - 0.226: 8 0.226 - 0.283: 16 Chirality restraints: 4876 Sorted by residual: chirality pdb=" CB VAL B1003 " pdb=" CA VAL B1003 " pdb=" CG1 VAL B1003 " pdb=" CG2 VAL B1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB VAL A1003 " pdb=" CA VAL A1003 " pdb=" CG1 VAL A1003 " pdb=" CG2 VAL A1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4873 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 700 " 0.053 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO C 701 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 701 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 701 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 700 " -0.053 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO D 701 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 701 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 701 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 700 " 0.053 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 701 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 701 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 701 " 0.044 5.00e-02 4.00e+02 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 9638 2.83 - 3.35: 28032 3.35 - 3.87: 48788 3.87 - 4.38: 55027 4.38 - 4.90: 95099 Nonbonded interactions: 236584 Sorted by model distance: nonbonded pdb=" OG1 THR C 21 " pdb=" OE2 GLU C 70 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR B 21 " pdb=" OE2 GLU B 70 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR A 21 " pdb=" OE2 GLU A 70 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR D 21 " pdb=" OE2 GLU D 70 " model vdw 2.319 3.040 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.322 3.040 ... (remaining 236579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.007 0.082 31748 Z= 0.351 Angle : 1.003 19.959 43092 Z= 0.591 Chirality : 0.052 0.283 4876 Planarity : 0.007 0.078 5424 Dihedral : 9.822 78.706 11412 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.25 % Allowed : 2.37 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.09), residues: 3868 helix: -3.13 (0.06), residues: 2488 sheet: -1.66 (0.33), residues: 192 loop : -3.20 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1146 TYR 0.019 0.003 TYR B 228 PHE 0.023 0.003 PHE C 932 TRP 0.050 0.003 TRP C 816 HIS 0.011 0.002 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.35 (31744) covalent geometry : angle 1.00285 / 0.59 (43084) SS BOND : bond 0.00790 / 0.47 ( 4) SS BOND : angle 1.79527 / 1.10 ( 8) hydrogen bonds : bond 0.21018 / 14.07 ( 1824) hydrogen bonds : angle 8.49384 / 5.88 ( 5412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 621 time to evaluate : 1.196 Fit side-chains REVERT: B 97 ARG cc_start: 0.6469 (mtt180) cc_final: 0.5883 (ttp-170) REVERT: B 258 VAL cc_start: 0.8166 (t) cc_final: 0.7929 (m) REVERT: B 338 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6567 (mmm160) REVERT: B 353 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7743 (tp30) REVERT: B 397 GLU cc_start: 0.7231 (tt0) cc_final: 0.7002 (tt0) REVERT: B 411 GLN cc_start: 0.8174 (tt0) cc_final: 0.7944 (tp-100) REVERT: B 519 TYR cc_start: 0.3645 (t80) cc_final: 0.3318 (t80) REVERT: B 851 ARG cc_start: 0.5591 (mtt180) cc_final: 0.5035 (mmp80) REVERT: B 1089 ARG cc_start: 0.5509 (mtt180) cc_final: 0.4999 (mmm160) REVERT: B 1138 ASP cc_start: 0.7763 (m-30) cc_final: 0.7525 (m-30) REVERT: A 17 LYS cc_start: 0.6741 (mtmp) cc_final: 0.6387 (ptmt) REVERT: A 97 ARG cc_start: 0.6433 (mtt180) cc_final: 0.5915 (ttp-170) REVERT: A 258 VAL cc_start: 0.8166 (t) cc_final: 0.7936 (m) REVERT: A 338 ARG cc_start: 0.7004 (mtt180) cc_final: 0.6564 (mmm160) REVERT: A 353 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7669 (tp30) REVERT: A 397 GLU cc_start: 0.7227 (tt0) cc_final: 0.7003 (tt0) REVERT: A 411 GLN cc_start: 0.8179 (tt0) cc_final: 0.7905 (tp-100) REVERT: A 519 TYR cc_start: 0.3664 (t80) cc_final: 0.3345 (t80) REVERT: A 851 ARG cc_start: 0.5608 (mtt180) cc_final: 0.5054 (mmp80) REVERT: A 1089 ARG cc_start: 0.5562 (mtt180) cc_final: 0.5040 (mmm160) REVERT: A 1138 ASP cc_start: 0.7772 (m-30) cc_final: 0.7534 (m-30) REVERT: C 97 ARG cc_start: 0.6584 (mtt180) cc_final: 0.5975 (ttp-170) REVERT: C 258 VAL cc_start: 0.8179 (t) cc_final: 0.7961 (m) REVERT: C 338 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6801 (mmp-170) REVERT: C 353 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7747 (tp30) REVERT: C 397 GLU cc_start: 0.7204 (tt0) cc_final: 0.6986 (tt0) REVERT: C 411 GLN cc_start: 0.8179 (tt0) cc_final: 0.7946 (tp-100) REVERT: C 851 ARG cc_start: 0.5873 (mtt180) cc_final: 0.5205 (mmp80) REVERT: C 1053 TYR cc_start: 0.7437 (t80) cc_final: 0.7233 (t80) REVERT: C 1138 ASP cc_start: 0.7775 (m-30) cc_final: 0.7563 (m-30) REVERT: D 97 ARG cc_start: 0.6468 (mtt180) cc_final: 0.5885 (ttp-170) REVERT: D 258 VAL cc_start: 0.8148 (t) cc_final: 0.7923 (m) REVERT: D 338 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6576 (mmm160) REVERT: D 353 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7746 (tp30) REVERT: D 397 GLU cc_start: 0.7219 (tt0) cc_final: 0.6991 (tt0) REVERT: D 411 GLN cc_start: 0.8196 (tt0) cc_final: 0.7958 (tp-100) REVERT: D 519 TYR cc_start: 0.3582 (t80) cc_final: 0.3279 (t80) REVERT: D 851 ARG cc_start: 0.5616 (mtt180) cc_final: 0.5073 (mmp80) REVERT: D 1089 ARG cc_start: 0.5519 (mtt180) cc_final: 0.4993 (mmm160) REVERT: D 1138 ASP cc_start: 0.7768 (m-30) cc_final: 0.7538 (m-30) outliers start: 8 outliers final: 4 residues processed: 629 average time/residue: 0.2589 time to fit residues: 238.7469 Evaluate side-chains 305 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 301 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain D residue 86 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS B 132 GLN B 160 HIS B 349 GLN B 405 ASN B 425 HIS B 570 ASN B 633 ASN B 861 ASN B 904 HIS B1010 GLN B1013 ASN A 88 HIS A 132 GLN A 160 HIS A 349 GLN A 405 ASN A 425 HIS A 570 ASN A 633 ASN A 861 ASN A 904 HIS A1010 GLN A1013 ASN C 88 HIS C 132 GLN C 160 HIS C 349 GLN C 405 ASN C 425 HIS C 570 ASN C 633 ASN C 782 ASN C 827 GLN C 861 ASN C 904 HIS C1010 GLN C1013 ASN D 88 HIS D 132 GLN D 160 HIS D 349 GLN D 405 ASN D 425 HIS D 570 ASN D 633 ASN D 861 ASN D 904 HIS D1010 GLN D1013 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.127289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096167 restraints weight = 74961.898| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.80 r_work: 0.3299 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 31748 Z= 0.176 Angle : 0.645 8.756 43092 Z= 0.335 Chirality : 0.039 0.152 4876 Planarity : 0.006 0.058 5424 Dihedral : 6.017 85.421 4324 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.34 % Allowed : 6.47 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.12), residues: 3868 helix: -0.23 (0.09), residues: 2528 sheet: -1.41 (0.32), residues: 232 loop : -2.84 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 337 TYR 0.015 0.002 TYR A 104 PHE 0.015 0.002 PHE C 793 TRP 0.029 0.002 TRP C 691 HIS 0.005 0.001 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (31744) covalent geometry : angle 0.64476 / 0.33 (43084) SS BOND : bond 0.00262 / 0.16 ( 4) SS BOND : angle 1.32072 / 0.80 ( 8) hydrogen bonds : bond 0.05516 / 3.75 ( 1824) hydrogen bonds : angle 4.81757 / 3.32 ( 5412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.6787 (mtt180) cc_final: 0.5976 (ttp-170) REVERT: B 123 LEU cc_start: 0.6978 (mt) cc_final: 0.5997 (mm) REVERT: B 156 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8435 (p) REVERT: B 258 VAL cc_start: 0.8081 (t) cc_final: 0.7867 (m) REVERT: B 353 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7728 (tp30) REVERT: B 400 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8875 (mt) REVERT: B 411 GLN cc_start: 0.8600 (tt0) cc_final: 0.8171 (tp-100) REVERT: B 519 TYR cc_start: 0.3951 (t80) cc_final: 0.3444 (t80) REVERT: B 851 ARG cc_start: 0.5930 (mtt180) cc_final: 0.5209 (mmp80) REVERT: B 1138 ASP cc_start: 0.8363 (m-30) cc_final: 0.8097 (m-30) REVERT: A 97 ARG cc_start: 0.6775 (mtt180) cc_final: 0.5997 (ttp-170) REVERT: A 123 LEU cc_start: 0.6973 (mt) cc_final: 0.6018 (mm) REVERT: A 156 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 258 VAL cc_start: 0.8081 (t) cc_final: 0.7865 (m) REVERT: A 353 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7705 (tp30) REVERT: A 400 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8874 (mt) REVERT: A 411 GLN cc_start: 0.8592 (tt0) cc_final: 0.8141 (tp-100) REVERT: A 519 TYR cc_start: 0.3748 (t80) cc_final: 0.3275 (t80) REVERT: A 851 ARG cc_start: 0.5948 (mtt180) cc_final: 0.5255 (mmp80) REVERT: A 893 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 1089 ARG cc_start: 0.5256 (mtt180) cc_final: 0.4602 (mmm160) REVERT: A 1138 ASP cc_start: 0.8355 (m-30) cc_final: 0.8085 (m-30) REVERT: C 93 ARG cc_start: 0.4874 (tmt90) cc_final: 0.4440 (ttm170) REVERT: C 97 ARG cc_start: 0.6787 (mtt180) cc_final: 0.5969 (ttp-170) REVERT: C 123 LEU cc_start: 0.7028 (mt) cc_final: 0.6560 (mm) REVERT: C 156 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8461 (p) REVERT: C 258 VAL cc_start: 0.8048 (t) cc_final: 0.7843 (m) REVERT: C 353 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7780 (tp30) REVERT: C 400 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8909 (mt) REVERT: C 411 GLN cc_start: 0.8593 (tt0) cc_final: 0.8147 (tp-100) REVERT: C 814 TYR cc_start: 0.8368 (m-10) cc_final: 0.7688 (m-80) REVERT: C 851 ARG cc_start: 0.6150 (mtt180) cc_final: 0.5330 (mmp80) REVERT: C 1089 ARG cc_start: 0.5286 (mtt180) cc_final: 0.4651 (mmm160) REVERT: C 1138 ASP cc_start: 0.8392 (m-30) cc_final: 0.8135 (m-30) REVERT: D 97 ARG cc_start: 0.6749 (mtt180) cc_final: 0.5941 (ttp-170) REVERT: D 123 LEU cc_start: 0.6778 (mt) cc_final: 0.5974 (mm) REVERT: D 156 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8442 (p) REVERT: D 258 VAL cc_start: 0.8098 (t) cc_final: 0.7890 (m) REVERT: D 353 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7801 (tp30) REVERT: D 400 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8893 (mt) REVERT: D 411 GLN cc_start: 0.8580 (tt0) cc_final: 0.8158 (tp-100) REVERT: D 519 TYR cc_start: 0.3968 (t80) cc_final: 0.3474 (t80) REVERT: D 851 ARG cc_start: 0.5924 (mtt180) cc_final: 0.5209 (mmp80) REVERT: D 893 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9120 (tp) REVERT: D 1089 ARG cc_start: 0.5212 (mtt180) cc_final: 0.4550 (mmm160) REVERT: D 1138 ASP cc_start: 0.8346 (m-30) cc_final: 0.8082 (m-30) outliers start: 76 outliers final: 47 residues processed: 404 average time/residue: 0.2277 time to fit residues: 141.4226 Evaluate side-chains 303 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 164 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 382 optimal weight: 0.6980 chunk 16 optimal weight: 30.0000 chunk 300 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 226 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS B1010 GLN A 88 HIS A1010 GLN C 88 HIS C1010 GLN C1080 HIS D 88 HIS D1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.125087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093521 restraints weight = 74857.687| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.58 r_work: 0.3268 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31748 Z= 0.208 Angle : 0.647 7.658 43092 Z= 0.333 Chirality : 0.040 0.163 4876 Planarity : 0.005 0.061 5424 Dihedral : 5.767 85.612 4324 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.62 % Allowed : 7.74 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3868 helix: 0.86 (0.10), residues: 2536 sheet: -1.08 (0.34), residues: 208 loop : -2.72 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1146 TYR 0.019 0.002 TYR C 339 PHE 0.020 0.002 PHE C 793 TRP 0.017 0.002 TRP C 691 HIS 0.006 0.002 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (31744) covalent geometry : angle 0.64682 / 0.33 (43084) SS BOND : bond 0.00342 / 0.21 ( 4) SS BOND : angle 1.35828 / 0.82 ( 8) hydrogen bonds : bond 0.05597 / 3.80 ( 1824) hydrogen bonds : angle 4.52834 / 3.13 ( 5412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 254 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 ARG cc_start: 0.6765 (mtt180) cc_final: 0.5891 (ttp-170) REVERT: B 156 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8471 (p) REVERT: B 200 MET cc_start: 0.6852 (ttp) cc_final: 0.6621 (ttp) REVERT: B 258 VAL cc_start: 0.8164 (t) cc_final: 0.7895 (m) REVERT: B 353 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7751 (tp30) REVERT: B 356 MET cc_start: 0.6544 (mmm) cc_final: 0.6072 (mmm) REVERT: B 519 TYR cc_start: 0.3689 (t80) cc_final: 0.3324 (t80) REVERT: B 691 TRP cc_start: 0.7895 (p-90) cc_final: 0.7606 (p-90) REVERT: B 851 ARG cc_start: 0.6213 (mtt180) cc_final: 0.5478 (mmp80) REVERT: B 1089 ARG cc_start: 0.5424 (mtt180) cc_final: 0.4656 (mmm160) REVERT: A 97 ARG cc_start: 0.6811 (mtt180) cc_final: 0.6001 (ttp-170) REVERT: A 156 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 200 MET cc_start: 0.7001 (ttp) cc_final: 0.6766 (ttp) REVERT: A 258 VAL cc_start: 0.8190 (t) cc_final: 0.7942 (m) REVERT: A 353 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7635 (tp30) REVERT: A 356 MET cc_start: 0.6499 (mmm) cc_final: 0.6014 (mmm) REVERT: A 519 TYR cc_start: 0.3676 (t80) cc_final: 0.3309 (t80) REVERT: A 691 TRP cc_start: 0.7877 (p-90) cc_final: 0.7580 (p-90) REVERT: A 851 ARG cc_start: 0.6258 (mtt180) cc_final: 0.5436 (mmp80) REVERT: A 1089 ARG cc_start: 0.5300 (mtt180) cc_final: 0.4568 (mmm160) REVERT: C 93 ARG cc_start: 0.4927 (tmt90) cc_final: 0.4662 (ttm170) REVERT: C 97 ARG cc_start: 0.6766 (mtt180) cc_final: 0.5913 (ttp-170) REVERT: C 156 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 258 VAL cc_start: 0.8164 (t) cc_final: 0.7906 (m) REVERT: C 353 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7691 (tp30) REVERT: C 400 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8943 (mt) REVERT: C 691 TRP cc_start: 0.7891 (p-90) cc_final: 0.7431 (p-90) REVERT: C 851 ARG cc_start: 0.6155 (mtt180) cc_final: 0.5341 (mmp80) REVERT: C 1089 ARG cc_start: 0.5361 (mtt180) cc_final: 0.4682 (mmm160) REVERT: D 97 ARG cc_start: 0.6744 (mtt180) cc_final: 0.5889 (ttp-170) REVERT: D 156 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8468 (p) REVERT: D 200 MET cc_start: 0.6957 (ttp) cc_final: 0.6740 (ttp) REVERT: D 258 VAL cc_start: 0.8151 (t) cc_final: 0.7885 (m) REVERT: D 353 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7773 (tp30) REVERT: D 356 MET cc_start: 0.6632 (mmm) cc_final: 0.6152 (mmm) REVERT: D 519 TYR cc_start: 0.3885 (t80) cc_final: 0.3501 (t80) REVERT: D 691 TRP cc_start: 0.7959 (p-90) cc_final: 0.7600 (p-90) REVERT: D 851 ARG cc_start: 0.6216 (mtt180) cc_final: 0.5494 (mmp80) REVERT: D 1089 ARG cc_start: 0.5316 (mtt180) cc_final: 0.4568 (mmm160) outliers start: 85 outliers final: 49 residues processed: 324 average time/residue: 0.2183 time to fit residues: 110.5494 Evaluate side-chains 271 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 390 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 371 optimal weight: 0.8980 chunk 267 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 231 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS A 88 HIS C 88 HIS C1080 HIS D 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.127028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094539 restraints weight = 73276.581| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.42 r_work: 0.3307 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31748 Z= 0.147 Angle : 0.567 7.594 43092 Z= 0.291 Chirality : 0.038 0.154 4876 Planarity : 0.004 0.056 5424 Dihedral : 5.477 81.507 4324 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.90 % Allowed : 8.23 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3868 helix: 1.42 (0.11), residues: 2540 sheet: -1.28 (0.32), residues: 236 loop : -2.59 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 416 TYR 0.016 0.001 TYR A 339 PHE 0.014 0.001 PHE C 793 TRP 0.013 0.001 TRP B 680 HIS 0.011 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (31744) covalent geometry : angle 0.56698 / 0.29 (43084) SS BOND : bond 0.00327 / 0.20 ( 4) SS BOND : angle 0.96775 / 0.58 ( 8) hydrogen bonds : bond 0.04672 / 3.18 ( 1824) hydrogen bonds : angle 4.23339 / 2.92 ( 5412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 241 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.6782 (mtt180) cc_final: 0.5852 (ttp-110) REVERT: B 156 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8605 (p) REVERT: B 200 MET cc_start: 0.7033 (ttp) cc_final: 0.6819 (ttp) REVERT: B 258 VAL cc_start: 0.8103 (t) cc_final: 0.7821 (m) REVERT: B 353 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7627 (tp30) REVERT: B 519 TYR cc_start: 0.3779 (t80) cc_final: 0.3386 (t80) REVERT: B 691 TRP cc_start: 0.7932 (p-90) cc_final: 0.7565 (p-90) REVERT: B 851 ARG cc_start: 0.6306 (mtt180) cc_final: 0.5615 (mmp80) REVERT: B 1089 ARG cc_start: 0.5314 (mtt180) cc_final: 0.4502 (mmm160) REVERT: A 97 ARG cc_start: 0.6778 (mtt180) cc_final: 0.5946 (ttp-170) REVERT: A 156 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8607 (p) REVERT: A 258 VAL cc_start: 0.8135 (t) cc_final: 0.7846 (m) REVERT: A 353 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7592 (tp30) REVERT: A 519 TYR cc_start: 0.3780 (t80) cc_final: 0.3386 (t80) REVERT: A 691 TRP cc_start: 0.7934 (p-90) cc_final: 0.7631 (p-90) REVERT: A 851 ARG cc_start: 0.6036 (mtt180) cc_final: 0.5233 (mmp80) REVERT: A 1089 ARG cc_start: 0.5153 (mtt180) cc_final: 0.4330 (mmm160) REVERT: C 93 ARG cc_start: 0.4954 (tmt90) cc_final: 0.4720 (ttm170) REVERT: C 97 ARG cc_start: 0.6794 (mtt180) cc_final: 0.5896 (ttp-170) REVERT: C 156 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8515 (p) REVERT: C 258 VAL cc_start: 0.8135 (t) cc_final: 0.7867 (m) REVERT: C 353 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7661 (tp30) REVERT: C 400 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8846 (mt) REVERT: C 691 TRP cc_start: 0.7924 (p-90) cc_final: 0.7538 (p-90) REVERT: C 851 ARG cc_start: 0.5841 (mtt180) cc_final: 0.5055 (mmp80) REVERT: C 1089 ARG cc_start: 0.5254 (mtt180) cc_final: 0.4515 (mmm160) REVERT: D 97 ARG cc_start: 0.6792 (mtt180) cc_final: 0.5877 (ttp-170) REVERT: D 156 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8600 (p) REVERT: D 258 VAL cc_start: 0.8109 (t) cc_final: 0.7826 (m) REVERT: D 353 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7619 (tp30) REVERT: D 519 TYR cc_start: 0.3886 (t80) cc_final: 0.3492 (t80) REVERT: D 691 TRP cc_start: 0.7914 (p-90) cc_final: 0.7544 (p-90) REVERT: D 851 ARG cc_start: 0.6316 (mtt180) cc_final: 0.5621 (mmp80) REVERT: D 1089 ARG cc_start: 0.5290 (mtt180) cc_final: 0.4508 (mmm160) outliers start: 94 outliers final: 69 residues processed: 309 average time/residue: 0.2095 time to fit residues: 102.9638 Evaluate side-chains 289 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 215 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 854 LEU Chi-restraints excluded: chain D residue 896 MET Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 199 optimal weight: 30.0000 chunk 346 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 338 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 7 optimal weight: 0.0470 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 242 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS A 88 HIS C 88 HIS C1080 HIS D 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.126463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.093832 restraints weight = 73747.918| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.45 r_work: 0.3294 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31748 Z= 0.163 Angle : 0.573 8.299 43092 Z= 0.293 Chirality : 0.039 0.150 4876 Planarity : 0.004 0.054 5424 Dihedral : 5.394 80.561 4324 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.87 % Allowed : 9.53 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3868 helix: 1.67 (0.11), residues: 2540 sheet: -1.24 (0.33), residues: 236 loop : -2.53 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 949 TYR 0.015 0.001 TYR A 339 PHE 0.020 0.001 PHE D 91 TRP 0.013 0.001 TRP A 680 HIS 0.009 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (31744) covalent geometry : angle 0.57242 / 0.29 (43084) SS BOND : bond 0.00293 / 0.17 ( 4) SS BOND : angle 0.96984 / 0.57 ( 8) hydrogen bonds : bond 0.04743 / 3.23 ( 1824) hydrogen bonds : angle 4.19826 / 2.90 ( 5412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 225 time to evaluate : 1.714 Fit side-chains REVERT: B 87 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7411 (ptmm) REVERT: B 97 ARG cc_start: 0.6732 (mtt180) cc_final: 0.5912 (ttp-170) REVERT: B 156 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8617 (p) REVERT: B 258 VAL cc_start: 0.8218 (t) cc_final: 0.7944 (m) REVERT: B 353 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7622 (tp30) REVERT: B 519 TYR cc_start: 0.4047 (t80) cc_final: 0.3645 (t80) REVERT: B 691 TRP cc_start: 0.7948 (p-90) cc_final: 0.7650 (p-90) REVERT: B 851 ARG cc_start: 0.6388 (mtt180) cc_final: 0.5671 (mmp80) REVERT: B 1089 ARG cc_start: 0.5264 (mtt180) cc_final: 0.4407 (mmm160) REVERT: A 87 LYS cc_start: 0.7865 (mmmm) cc_final: 0.7384 (ptmm) REVERT: A 97 ARG cc_start: 0.6723 (mtt180) cc_final: 0.5889 (ttp-170) REVERT: A 156 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8617 (p) REVERT: A 258 VAL cc_start: 0.8151 (t) cc_final: 0.7876 (m) REVERT: A 353 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7593 (tp30) REVERT: A 519 TYR cc_start: 0.4049 (t80) cc_final: 0.3656 (t80) REVERT: A 691 TRP cc_start: 0.7946 (p-90) cc_final: 0.7655 (p-90) REVERT: A 851 ARG cc_start: 0.6102 (mtt180) cc_final: 0.5229 (mmp80) REVERT: A 1089 ARG cc_start: 0.5260 (mtt180) cc_final: 0.4398 (mmm160) REVERT: C 87 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7411 (ptmm) REVERT: C 97 ARG cc_start: 0.6743 (mtt180) cc_final: 0.5930 (ttp-170) REVERT: C 156 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8536 (p) REVERT: C 258 VAL cc_start: 0.8150 (t) cc_final: 0.7891 (m) REVERT: C 353 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7624 (tp30) REVERT: C 400 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8843 (mt) REVERT: C 691 TRP cc_start: 0.7935 (p-90) cc_final: 0.7543 (p-90) REVERT: C 851 ARG cc_start: 0.5816 (mtt180) cc_final: 0.5026 (mmp80) REVERT: C 1089 ARG cc_start: 0.5186 (mtt180) cc_final: 0.4451 (mmm160) REVERT: D 87 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7389 (ptmm) REVERT: D 97 ARG cc_start: 0.6727 (mtt180) cc_final: 0.5912 (ttp-170) REVERT: D 156 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8613 (p) REVERT: D 258 VAL cc_start: 0.8220 (t) cc_final: 0.7945 (m) REVERT: D 353 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7693 (tp30) REVERT: D 519 TYR cc_start: 0.3997 (t80) cc_final: 0.3609 (t80) REVERT: D 691 TRP cc_start: 0.7932 (p-90) cc_final: 0.7633 (p-90) REVERT: D 851 ARG cc_start: 0.6395 (mtt180) cc_final: 0.5675 (mmp80) REVERT: D 1089 ARG cc_start: 0.5239 (mtt180) cc_final: 0.4389 (mmm160) outliers start: 93 outliers final: 70 residues processed: 297 average time/residue: 0.2092 time to fit residues: 99.8875 Evaluate side-chains 278 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 203 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 854 LEU Chi-restraints excluded: chain D residue 896 MET Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 333 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 317 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS A 88 HIS A 90 ASN C 88 HIS C 90 ASN C1080 HIS D 88 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.127207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094711 restraints weight = 73362.279| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.43 r_work: 0.3309 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31748 Z= 0.135 Angle : 0.537 6.546 43092 Z= 0.276 Chirality : 0.038 0.146 4876 Planarity : 0.004 0.052 5424 Dihedral : 5.246 77.342 4324 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.93 % Allowed : 10.05 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3868 helix: 1.91 (0.11), residues: 2540 sheet: -1.20 (0.33), residues: 236 loop : -2.42 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 949 TYR 0.015 0.001 TYR C 339 PHE 0.014 0.001 PHE D 91 TRP 0.012 0.001 TRP D 680 HIS 0.008 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (31744) covalent geometry : angle 0.53691 / 0.28 (43084) SS BOND : bond 0.00263 / 0.16 ( 4) SS BOND : angle 0.82387 / 0.50 ( 8) hydrogen bonds : bond 0.04373 / 2.97 ( 1824) hydrogen bonds : angle 4.06816 / 2.80 ( 5412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 234 time to evaluate : 1.079 Fit side-chains REVERT: B 87 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7479 (ptmm) REVERT: B 97 ARG cc_start: 0.6731 (mtt180) cc_final: 0.5899 (ttp-170) REVERT: B 156 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8627 (p) REVERT: B 258 VAL cc_start: 0.8162 (t) cc_final: 0.7877 (m) REVERT: B 353 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7643 (tp30) REVERT: B 519 TYR cc_start: 0.3933 (t80) cc_final: 0.3506 (t80) REVERT: B 691 TRP cc_start: 0.7932 (p-90) cc_final: 0.7704 (p-90) REVERT: B 786 TYR cc_start: 0.8820 (t80) cc_final: 0.8542 (t80) REVERT: B 851 ARG cc_start: 0.6186 (mtt180) cc_final: 0.5488 (mmp80) REVERT: B 1089 ARG cc_start: 0.5248 (mtt180) cc_final: 0.4405 (mmm160) REVERT: A 87 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7480 (ptmm) REVERT: A 97 ARG cc_start: 0.6725 (mtt180) cc_final: 0.5878 (ttp-170) REVERT: A 156 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8624 (p) REVERT: A 258 VAL cc_start: 0.8160 (t) cc_final: 0.7879 (m) REVERT: A 353 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7563 (tp30) REVERT: A 354 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.5791 (ttm110) REVERT: A 519 TYR cc_start: 0.3937 (t80) cc_final: 0.3513 (t80) REVERT: A 691 TRP cc_start: 0.7923 (p-90) cc_final: 0.7681 (p-90) REVERT: A 851 ARG cc_start: 0.6158 (mtt180) cc_final: 0.5253 (mmp80) REVERT: A 1089 ARG cc_start: 0.5252 (mtt180) cc_final: 0.4441 (mmm160) REVERT: C 87 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7471 (ptmm) REVERT: C 97 ARG cc_start: 0.6731 (mtt180) cc_final: 0.5912 (ttp-170) REVERT: C 156 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8600 (p) REVERT: C 258 VAL cc_start: 0.8166 (t) cc_final: 0.7897 (m) REVERT: C 353 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7661 (tp30) REVERT: C 400 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8880 (mt) REVERT: C 691 TRP cc_start: 0.7922 (p-90) cc_final: 0.7601 (p-90) REVERT: C 851 ARG cc_start: 0.5925 (mtt180) cc_final: 0.5146 (mmp80) REVERT: C 1089 ARG cc_start: 0.5219 (mtt180) cc_final: 0.4400 (mmm160) REVERT: D 87 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7468 (ptmm) REVERT: D 97 ARG cc_start: 0.6647 (mtt180) cc_final: 0.5864 (ttp-170) REVERT: D 156 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8661 (p) REVERT: D 258 VAL cc_start: 0.8161 (t) cc_final: 0.7879 (m) REVERT: D 353 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7645 (tp30) REVERT: D 519 TYR cc_start: 0.4136 (t80) cc_final: 0.3749 (t80) REVERT: D 691 TRP cc_start: 0.7917 (p-90) cc_final: 0.7698 (p-90) REVERT: D 786 TYR cc_start: 0.8824 (t80) cc_final: 0.8550 (t80) REVERT: D 851 ARG cc_start: 0.6196 (mtt180) cc_final: 0.5493 (mmp80) REVERT: D 1089 ARG cc_start: 0.5289 (mtt180) cc_final: 0.4372 (mmm160) outliers start: 95 outliers final: 67 residues processed: 307 average time/residue: 0.2005 time to fit residues: 98.4659 Evaluate side-chains 295 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 222 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 896 MET Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 854 LEU Chi-restraints excluded: chain D residue 896 MET Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1081 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 47 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 298 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 339 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS B 584 ASN A 88 HIS C 88 HIS C 827 GLN C1080 HIS D 88 HIS D 584 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096622 restraints weight = 73768.789| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.45 r_work: 0.3342 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31748 Z= 0.100 Angle : 0.495 8.245 43092 Z= 0.255 Chirality : 0.037 0.151 4876 Planarity : 0.004 0.054 5424 Dihedral : 4.993 74.144 4324 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.03 % Allowed : 11.37 % Favored : 86.59 % 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 are not related in a simple way. whole: 1.21 (0.14), residues: 3868 helix: 2.20 (0.11), residues: 2540 sheet: -1.15 (0.32), residues: 236 loop : -2.28 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 949 TYR 0.020 0.001 TYR D 339 PHE 0.014 0.001 PHE D 91 TRP 0.011 0.001 TRP A 691 HIS 0.013 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (31744) covalent geometry : angle 0.49522 / 0.25 (43084) SS BOND : bond 0.00189 / 0.11 ( 4) SS BOND : angle 0.60147 / 0.37 ( 8) hydrogen bonds : bond 0.03674 / 2.50 ( 1824) hydrogen bonds : angle 3.83997 / 2.64 ( 5412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 265 time to evaluate : 1.206 Fit side-chains REVERT: B 87 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7475 (ptmm) REVERT: B 97 ARG cc_start: 0.6601 (mtt180) cc_final: 0.5842 (ttp-110) REVERT: B 156 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8613 (p) REVERT: B 258 VAL cc_start: 0.8194 (t) cc_final: 0.7809 (m) REVERT: B 353 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7658 (tp30) REVERT: B 519 TYR cc_start: 0.3885 (t80) cc_final: 0.3445 (t80) REVERT: B 786 TYR cc_start: 0.8762 (t80) cc_final: 0.8457 (t80) REVERT: B 851 ARG cc_start: 0.6168 (mtt180) cc_final: 0.5495 (mmp80) REVERT: B 1089 ARG cc_start: 0.5141 (mtt180) cc_final: 0.4301 (mmm160) REVERT: A 87 LYS cc_start: 0.7798 (mmmm) cc_final: 0.7490 (ptmm) REVERT: A 97 ARG cc_start: 0.6673 (mtt180) cc_final: 0.5831 (ttp-110) REVERT: A 156 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 258 VAL cc_start: 0.8167 (t) cc_final: 0.7793 (m) REVERT: A 353 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7598 (tp30) REVERT: A 519 TYR cc_start: 0.3885 (t80) cc_final: 0.3449 (t80) REVERT: A 851 ARG cc_start: 0.6259 (mtt180) cc_final: 0.5340 (mmp80) REVERT: A 1089 ARG cc_start: 0.5139 (mtt180) cc_final: 0.4297 (mmm160) REVERT: C 87 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7507 (ptmm) REVERT: C 93 ARG cc_start: 0.5012 (tmt90) cc_final: 0.4755 (ttm170) REVERT: C 97 ARG cc_start: 0.6626 (mtt180) cc_final: 0.5856 (ttp-170) REVERT: C 156 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 258 VAL cc_start: 0.8159 (t) cc_final: 0.7874 (m) REVERT: C 353 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7707 (tp30) REVERT: C 356 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5836 (mmm) REVERT: C 691 TRP cc_start: 0.7890 (p-90) cc_final: 0.7646 (p-90) REVERT: C 851 ARG cc_start: 0.5926 (mtt180) cc_final: 0.5146 (mmp80) REVERT: C 1089 ARG cc_start: 0.5202 (mtt180) cc_final: 0.4387 (mmm160) REVERT: D 87 LYS cc_start: 0.7832 (mmmm) cc_final: 0.7508 (ptmm) REVERT: D 97 ARG cc_start: 0.6626 (mtt180) cc_final: 0.5849 (ttp-110) REVERT: D 156 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8610 (p) REVERT: D 258 VAL cc_start: 0.8199 (t) cc_final: 0.7821 (m) REVERT: D 353 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7649 (tp30) REVERT: D 519 TYR cc_start: 0.3882 (t80) cc_final: 0.3447 (t80) REVERT: D 786 TYR cc_start: 0.8765 (t80) cc_final: 0.8467 (t80) REVERT: D 851 ARG cc_start: 0.6178 (mtt180) cc_final: 0.5500 (mmp80) REVERT: D 1089 ARG cc_start: 0.5115 (mtt180) cc_final: 0.4284 (mmm160) outliers start: 66 outliers final: 50 residues processed: 314 average time/residue: 0.2041 time to fit residues: 103.0347 Evaluate side-chains 285 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1008 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 102 optimal weight: 0.0010 chunk 167 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 316 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 chunk 284 optimal weight: 6.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS B 260 GLN A 88 HIS A 260 GLN A 584 ASN C 88 HIS C 584 ASN C1080 HIS D 88 HIS D 260 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095620 restraints weight = 73550.652| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.45 r_work: 0.3326 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31748 Z= 0.117 Angle : 0.518 8.453 43092 Z= 0.266 Chirality : 0.037 0.151 4876 Planarity : 0.004 0.051 5424 Dihedral : 4.959 74.031 4324 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 11.68 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3868 helix: 2.28 (0.11), residues: 2536 sheet: -1.12 (0.33), residues: 236 loop : -2.25 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 949 TYR 0.018 0.001 TYR D 339 PHE 0.010 0.001 PHE C 793 TRP 0.049 0.001 TRP B 691 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (31744) covalent geometry : angle 0.51755 / 0.27 (43084) SS BOND : bond 0.00198 / 0.12 ( 4) SS BOND : angle 0.62543 / 0.38 ( 8) hydrogen bonds : bond 0.03886 / 2.64 ( 1824) hydrogen bonds : angle 3.86083 / 2.65 ( 5412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 239 time to evaluate : 1.275 Fit side-chains REVERT: B 87 LYS cc_start: 0.7612 (mmmm) cc_final: 0.7401 (ptmm) REVERT: B 97 ARG cc_start: 0.6630 (mtt180) cc_final: 0.5842 (ttp-110) REVERT: B 156 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8608 (p) REVERT: B 258 VAL cc_start: 0.8065 (t) cc_final: 0.7807 (m) REVERT: B 353 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7640 (tp30) REVERT: B 519 TYR cc_start: 0.3979 (t80) cc_final: 0.3568 (t80) REVERT: B 648 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8233 (tt) REVERT: B 786 TYR cc_start: 0.8796 (t80) cc_final: 0.8483 (t80) REVERT: B 851 ARG cc_start: 0.6024 (mtt180) cc_final: 0.5376 (mmp80) REVERT: B 1089 ARG cc_start: 0.5155 (mtt180) cc_final: 0.4313 (mmm160) REVERT: A 87 LYS cc_start: 0.7660 (mmmm) cc_final: 0.7387 (ptmm) REVERT: A 97 ARG cc_start: 0.6734 (mtt180) cc_final: 0.5870 (ttp-110) REVERT: A 156 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 258 VAL cc_start: 0.8068 (t) cc_final: 0.7817 (m) REVERT: A 353 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7657 (tp30) REVERT: A 519 TYR cc_start: 0.3976 (t80) cc_final: 0.3563 (t80) REVERT: A 648 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8231 (tt) REVERT: A 851 ARG cc_start: 0.6106 (mtt180) cc_final: 0.5216 (mmp80) REVERT: A 1089 ARG cc_start: 0.5126 (mtt180) cc_final: 0.4298 (mmm160) REVERT: C 87 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7395 (ptmm) REVERT: C 93 ARG cc_start: 0.5044 (tmt90) cc_final: 0.4741 (ttm170) REVERT: C 97 ARG cc_start: 0.6660 (mtt180) cc_final: 0.5866 (ttp-170) REVERT: C 156 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 258 VAL cc_start: 0.8168 (t) cc_final: 0.7794 (m) REVERT: C 353 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7704 (tp30) REVERT: C 356 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5823 (mmm) REVERT: C 648 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8218 (tt) REVERT: C 691 TRP cc_start: 0.7910 (p-90) cc_final: 0.7657 (p-90) REVERT: C 851 ARG cc_start: 0.5860 (mtt180) cc_final: 0.5110 (mmp80) REVERT: C 1089 ARG cc_start: 0.5148 (mtt180) cc_final: 0.4308 (mmm160) REVERT: D 87 LYS cc_start: 0.7635 (mmmm) cc_final: 0.7411 (ptmm) REVERT: D 97 ARG cc_start: 0.6650 (mtt180) cc_final: 0.5850 (ttp-110) REVERT: D 156 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8610 (p) REVERT: D 258 VAL cc_start: 0.8061 (t) cc_final: 0.7802 (m) REVERT: D 353 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7642 (tp30) REVERT: D 519 TYR cc_start: 0.3981 (t80) cc_final: 0.3571 (t80) REVERT: D 648 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8237 (tt) REVERT: D 786 TYR cc_start: 0.8804 (t80) cc_final: 0.8493 (t80) REVERT: D 851 ARG cc_start: 0.6034 (mtt180) cc_final: 0.5378 (mmp80) REVERT: D 1089 ARG cc_start: 0.5135 (mtt180) cc_final: 0.4296 (mmm160) outliers start: 83 outliers final: 69 residues processed: 307 average time/residue: 0.2099 time to fit residues: 103.1940 Evaluate side-chains 305 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 227 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 854 LEU Chi-restraints excluded: chain D residue 896 MET Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 303 optimal weight: 20.0000 chunk 348 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 372 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 384 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS B 90 ASN A 88 HIS C 88 HIS C 260 GLN C1080 HIS D 88 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.126199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093316 restraints weight = 73638.138| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.43 r_work: 0.3288 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31748 Z= 0.184 Angle : 0.594 9.370 43092 Z= 0.302 Chirality : 0.040 0.240 4876 Planarity : 0.004 0.047 5424 Dihedral : 5.169 75.650 4324 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.53 % Allowed : 12.08 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.14), residues: 3868 helix: 2.12 (0.11), residues: 2532 sheet: -0.89 (0.35), residues: 208 loop : -2.29 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 949 TYR 0.020 0.002 TYR D 257 PHE 0.018 0.002 PHE C 793 TRP 0.044 0.001 TRP D 691 HIS 0.011 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (31744) covalent geometry : angle 0.59356 / 0.30 (43084) SS BOND : bond 0.00266 / 0.16 ( 4) SS BOND : angle 0.92179 / 0.54 ( 8) hydrogen bonds : bond 0.04755 / 3.23 ( 1824) hydrogen bonds : angle 4.07871 / 2.81 ( 5412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 222 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: B 87 LYS cc_start: 0.7551 (mmmm) cc_final: 0.7310 (ptmm) REVERT: B 97 ARG cc_start: 0.6709 (mtt180) cc_final: 0.5909 (ttp-170) REVERT: B 156 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8656 (p) REVERT: B 258 VAL cc_start: 0.8181 (t) cc_final: 0.7917 (m) REVERT: B 353 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7714 (tp30) REVERT: B 519 TYR cc_start: 0.4019 (t80) cc_final: 0.3631 (t80) REVERT: B 648 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 851 ARG cc_start: 0.6079 (mtt180) cc_final: 0.5374 (mmp80) REVERT: B 1089 ARG cc_start: 0.5152 (mtt180) cc_final: 0.4302 (mmm160) REVERT: A 87 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7408 (ptmm) REVERT: A 97 ARG cc_start: 0.6730 (mtt180) cc_final: 0.5887 (ttp-110) REVERT: A 156 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 258 VAL cc_start: 0.8124 (t) cc_final: 0.7852 (m) REVERT: A 353 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7644 (tp30) REVERT: A 519 TYR cc_start: 0.4015 (t80) cc_final: 0.3631 (t80) REVERT: A 648 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 851 ARG cc_start: 0.6165 (mtt180) cc_final: 0.5235 (mmp80) REVERT: A 1089 ARG cc_start: 0.5125 (mtt180) cc_final: 0.4271 (mmm160) REVERT: C 87 LYS cc_start: 0.7586 (mmmm) cc_final: 0.7384 (ptmm) REVERT: C 97 ARG cc_start: 0.6733 (mtt180) cc_final: 0.5921 (ttp-170) REVERT: C 156 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8608 (p) REVERT: C 258 VAL cc_start: 0.8106 (t) cc_final: 0.7871 (m) REVERT: C 353 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7711 (tp30) REVERT: C 648 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8332 (tt) REVERT: C 691 TRP cc_start: 0.7905 (p-90) cc_final: 0.7610 (p-90) REVERT: C 851 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5193 (mmp80) REVERT: C 1089 ARG cc_start: 0.5193 (mtt180) cc_final: 0.4323 (mmm160) REVERT: D 87 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7319 (ptmm) REVERT: D 97 ARG cc_start: 0.6731 (mtt180) cc_final: 0.5921 (ttp-170) REVERT: D 156 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8661 (p) REVERT: D 258 VAL cc_start: 0.8179 (t) cc_final: 0.7917 (m) REVERT: D 353 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7702 (tp30) REVERT: D 519 TYR cc_start: 0.4022 (t80) cc_final: 0.3640 (t80) REVERT: D 648 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8339 (tt) REVERT: D 851 ARG cc_start: 0.6095 (mtt180) cc_final: 0.5378 (mmp80) REVERT: D 1089 ARG cc_start: 0.5131 (mtt180) cc_final: 0.4284 (mmm160) outliers start: 82 outliers final: 67 residues processed: 289 average time/residue: 0.2122 time to fit residues: 97.6381 Evaluate side-chains 290 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 215 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 854 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 60 optimal weight: 7.9990 chunk 135 optimal weight: 0.0000 chunk 22 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 347 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS A 88 HIS C 88 HIS C1080 HIS D 88 HIS D 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.126954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094260 restraints weight = 73238.915| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.41 r_work: 0.3303 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31748 Z= 0.147 Angle : 0.563 9.586 43092 Z= 0.286 Chirality : 0.040 0.275 4876 Planarity : 0.004 0.048 5424 Dihedral : 5.106 74.364 4324 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.44 % Allowed : 12.39 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.14), residues: 3868 helix: 2.15 (0.11), residues: 2540 sheet: -1.05 (0.32), residues: 256 loop : -2.25 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 949 TYR 0.018 0.002 TYR B 339 PHE 0.014 0.001 PHE D 793 TRP 0.045 0.001 TRP A 691 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (31744) covalent geometry : angle 0.56340 / 0.29 (43084) SS BOND : bond 0.00251 / 0.15 ( 4) SS BOND : angle 0.77883 / 0.47 ( 8) hydrogen bonds : bond 0.04412 / 3.00 ( 1824) hydrogen bonds : angle 4.00227 / 2.76 ( 5412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 223 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: B 87 LYS cc_start: 0.7562 (mmmm) cc_final: 0.7347 (ptmm) REVERT: B 97 ARG cc_start: 0.6718 (mtt180) cc_final: 0.5909 (ttp-170) REVERT: B 156 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 258 VAL cc_start: 0.8203 (t) cc_final: 0.7936 (m) REVERT: B 353 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7698 (tp30) REVERT: B 519 TYR cc_start: 0.4023 (t80) cc_final: 0.3635 (t80) REVERT: B 648 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8358 (tt) REVERT: B 786 TYR cc_start: 0.8859 (t80) cc_final: 0.8572 (t80) REVERT: B 851 ARG cc_start: 0.6043 (mtt180) cc_final: 0.5356 (mmp80) REVERT: B 1089 ARG cc_start: 0.5183 (mtt180) cc_final: 0.4329 (mmm160) REVERT: A 87 LYS cc_start: 0.7576 (mmmm) cc_final: 0.7352 (ptmm) REVERT: A 97 ARG cc_start: 0.6677 (mtt180) cc_final: 0.5870 (tmm160) REVERT: A 156 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8643 (p) REVERT: A 258 VAL cc_start: 0.8169 (t) cc_final: 0.7903 (m) REVERT: A 353 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7637 (tp30) REVERT: A 519 TYR cc_start: 0.4008 (t80) cc_final: 0.3627 (t80) REVERT: A 648 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8355 (tt) REVERT: A 851 ARG cc_start: 0.6141 (mtt180) cc_final: 0.5200 (mmp80) REVERT: A 1089 ARG cc_start: 0.5238 (mtt180) cc_final: 0.4384 (mmm160) REVERT: C 97 ARG cc_start: 0.6755 (mtt180) cc_final: 0.5925 (ttp-170) REVERT: C 156 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8653 (p) REVERT: C 258 VAL cc_start: 0.8123 (t) cc_final: 0.7854 (m) REVERT: C 353 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7711 (tp30) REVERT: C 648 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8300 (tt) REVERT: C 691 TRP cc_start: 0.7919 (p-90) cc_final: 0.7606 (p-90) REVERT: C 851 ARG cc_start: 0.5933 (mtt180) cc_final: 0.5172 (mmp80) REVERT: C 1089 ARG cc_start: 0.5182 (mtt180) cc_final: 0.4330 (mmm160) REVERT: D 87 LYS cc_start: 0.7574 (mmmm) cc_final: 0.7337 (ptmm) REVERT: D 97 ARG cc_start: 0.6738 (mtt180) cc_final: 0.5920 (ttp-170) REVERT: D 156 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8657 (p) REVERT: D 258 VAL cc_start: 0.8207 (t) cc_final: 0.7943 (m) REVERT: D 353 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7701 (tp30) REVERT: D 519 TYR cc_start: 0.4012 (t80) cc_final: 0.3631 (t80) REVERT: D 648 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8371 (tt) REVERT: D 786 TYR cc_start: 0.8862 (t80) cc_final: 0.8575 (t80) REVERT: D 851 ARG cc_start: 0.6059 (mtt180) cc_final: 0.5322 (mmp80) REVERT: D 1089 ARG cc_start: 0.5165 (mtt180) cc_final: 0.4314 (mmm160) outliers start: 79 outliers final: 67 residues processed: 284 average time/residue: 0.2213 time to fit residues: 99.9583 Evaluate side-chains 290 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 215 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 854 LEU Chi-restraints excluded: chain D residue 896 MET Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 45 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 375 optimal weight: 0.9990 chunk 335 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 222 optimal weight: 30.0000 chunk 218 optimal weight: 20.0000 chunk 88 optimal weight: 0.0770 chunk 265 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS A 88 HIS C 88 HIS C1080 HIS D 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.128013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095531 restraints weight = 73527.783| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.44 r_work: 0.3321 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31748 Z= 0.115 Angle : 0.530 9.442 43092 Z= 0.269 Chirality : 0.038 0.264 4876 Planarity : 0.004 0.049 5424 Dihedral : 4.969 72.655 4324 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.50 % Allowed : 12.33 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3868 helix: 2.33 (0.11), residues: 2532 sheet: -0.98 (0.31), residues: 256 loop : -2.19 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 949 TYR 0.018 0.001 TYR A 339 PHE 0.011 0.001 PHE D 91 TRP 0.045 0.001 TRP A 691 HIS 0.008 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (31744) covalent geometry : angle 0.52994 / 0.27 (43084) SS BOND : bond 0.00208 / 0.12 ( 4) SS BOND : angle 0.60576 / 0.38 ( 8) hydrogen bonds : bond 0.03929 / 2.67 ( 1824) hydrogen bonds : angle 3.87061 / 2.67 ( 5412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8152.37 seconds wall clock time: 140 minutes 0.92 seconds (8400.92 seconds total)