Starting phenix.real_space_refine on Sun Aug 9 00:07:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30la_57866/08_2026/30la_57866.cif Found real_map, /net/cci-nas-00/data/ceres_data/30la_57866/08_2026/30la_57866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30la_57866/08_2026/30la_57866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30la_57866/08_2026/30la_57866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30la_57866/08_2026/30la_57866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30la_57866/08_2026/30la_57866.map" } resolution = 3.0 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= 0.011 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 Ca 4 9.91 5 S 152 5.16 5 C 19592 2.51 5 N 5344 2.21 5 O 5160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30252 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7562 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASP:plan': 15, 'HIS:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 217 Chain: "B" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7562 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASP:plan': 15, 'HIS:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 217 Chain: "C" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7562 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASP:plan': 15, 'HIS:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 217 Chain: "D" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7562 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASP:plan': 15, 'HIS:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 217 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.64, per 1000 atoms: 0.19 Number of scatterers: 30252 At special positions: 0 Unit cell: (139.689, 139.689, 153.384, 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) Ca 4 19.99 S 152 16.00 O 5160 8.00 N 5344 7.00 C 19592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.04 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.04 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7360 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 12 sheets defined 67.6% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 4.325A pdb=" N LYS A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.913A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.236A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.588A pdb=" N THR A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.653A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.595A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 3.988A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 4.025A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 421 through 436 removed outlier: 4.351A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.828A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 682 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.674A pdb=" N THR A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 777 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 905 Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 916 through 925 Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 974 removed outlier: 3.720A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.736A pdb=" N MET A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.860A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1050 through 1071 removed outlier: 4.393A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.302A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1177 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.899A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 4.291A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.661A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.562A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.982A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 4.011A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 421 through 436 removed outlier: 4.349A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.717A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 607 through 634 Processing helix chain 'B' and resid 634 through 644 removed outlier: 4.028A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 682 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.710A pdb=" N THR B 705 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 777 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 861 Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 905 Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 916 through 925 Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 974 removed outlier: 3.716A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 removed outlier: 3.704A pdb=" N MET B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.861A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1050 Processing helix chain 'B' and resid 1050 through 1071 removed outlier: 4.407A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.208A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1177 Processing helix chain 'C' and resid 9 through 15 removed outlier: 4.318A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.915A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 4.108A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.565A pdb=" N THR C 199 " --> pdb=" O ASN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.663A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.597A pdb=" N GLY C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 3.987A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 removed outlier: 4.023A pdb=" N GLY C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 421 through 436 removed outlier: 4.483A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.728A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 584 through 602 Processing helix chain 'C' and resid 607 through 634 Processing helix chain 'C' and resid 634 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 682 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 removed outlier: 3.654A pdb=" N THR C 705 " --> pdb=" O LEU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 777 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 861 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 905 Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 916 through 925 Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 975 removed outlier: 3.713A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 975 " --> pdb=" O TYR C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 removed outlier: 3.779A pdb=" N MET C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.874A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C1033 " --> pdb=" O LEU C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1050 Processing helix chain 'C' and resid 1050 through 1071 removed outlier: 4.402A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.215A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1177 Processing helix chain 'D' and resid 9 through 15 removed outlier: 4.314A pdb=" N LYS D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.924A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 4.113A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.664A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.595A pdb=" N GLY D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 removed outlier: 3.981A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 removed outlier: 4.016A pdb=" N GLY D 386 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 421 through 436 removed outlier: 4.454A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.964A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 584 through 602 Processing helix chain 'D' and resid 607 through 634 Processing helix chain 'D' and resid 634 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 682 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 removed outlier: 3.710A pdb=" N THR D 705 " --> pdb=" O LEU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 777 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 861 Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 905 Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 916 through 925 Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 974 removed outlier: 3.717A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 984 removed outlier: 3.721A pdb=" N MET D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.872A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE D1033 " --> pdb=" O LEU D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1050 Processing helix chain 'D' and resid 1050 through 1071 removed outlier: 4.381A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.212A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1177 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 3.644A pdb=" N THR A 68 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 8.042A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY A 156 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1000 through 1001 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.617A pdb=" N THR B 68 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 211 removed outlier: 8.083A pdb=" N TYR B 211 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA B 231 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY B 156 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1000 through 1001 Processing sheet with id=AA7, first strand: chain 'C' and resid 16 through 19 removed outlier: 3.645A pdb=" N THR C 68 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 210 through 211 removed outlier: 8.104A pdb=" N TYR C 211 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY C 156 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 301 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1000 through 1001 Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.645A pdb=" N THR D 68 " --> pdb=" O THR D 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 210 through 211 removed outlier: 8.105A pdb=" N TYR D 211 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA D 231 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY D 156 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 1000 through 1001 1902 hydrogen bonds defined for protein. 5577 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: 5.74 Time building geometry restraints manager: 3.20 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: 9821 1.34 - 1.47: 7502 1.47 - 1.59: 13397 1.59 - 1.72: 0 1.72 - 1.84: 228 Bond restraints: 30948 Sorted by residual: bond pdb=" C MET C 659 " pdb=" O MET C 659 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.35e-02 5.49e+03 1.82e+00 bond pdb=" CG ARG C 611 " pdb=" CD ARG C 611 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLN D1153 " pdb=" CG GLN D1153 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CG ARG B 171 " pdb=" CD ARG B 171 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB GLN A1153 " pdb=" CG GLN A1153 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.60e+00 ... (remaining 30943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 41768 3.47 - 6.95: 245 6.95 - 10.42: 35 10.42 - 13.89: 31 13.89 - 17.37: 5 Bond angle restraints: 42084 Sorted by residual: angle pdb=" C SER C 469 " pdb=" CA SER C 469 " pdb=" CB SER C 469 " ideal model delta sigma weight residual 116.54 110.02 6.52 1.15e+00 7.56e-01 3.22e+01 angle pdb=" CA LEU D 397 " pdb=" CB LEU D 397 " pdb=" CG LEU D 397 " ideal model delta sigma weight residual 116.30 133.67 -17.37 3.50e+00 8.16e-02 2.46e+01 angle pdb=" CB MET A 576 " pdb=" CG MET A 576 " pdb=" SD MET A 576 " ideal model delta sigma weight residual 112.70 126.75 -14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" CB MET C 576 " pdb=" CG MET C 576 " pdb=" SD MET C 576 " ideal model delta sigma weight residual 112.70 126.58 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CB LYS B 13 " pdb=" CG LYS B 13 " pdb=" CD LYS B 13 " ideal model delta sigma weight residual 111.30 121.75 -10.45 2.30e+00 1.89e-01 2.07e+01 ... (remaining 42079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 16375 17.86 - 35.73: 1456 35.73 - 53.59: 319 53.59 - 71.45: 34 71.45 - 89.32: 12 Dihedral angle restraints: 18196 sinusoidal: 6804 harmonic: 11392 Sorted by residual: dihedral pdb=" CA MET C 659 " pdb=" C MET C 659 " pdb=" N GLN C 660 " pdb=" CA GLN C 660 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET C 509 " pdb=" C MET C 509 " pdb=" N LEU C 510 " pdb=" CA LEU C 510 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET A 509 " pdb=" C MET A 509 " pdb=" N LEU A 510 " pdb=" CA LEU A 510 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 18193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4234 0.061 - 0.122: 564 0.122 - 0.183: 21 0.183 - 0.244: 4 0.244 - 0.305: 1 Chirality restraints: 4824 Sorted by residual: chirality pdb=" CG LEU A 567 " pdb=" CB LEU A 567 " pdb=" CD1 LEU A 567 " pdb=" CD2 LEU A 567 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CG LEU D 567 " pdb=" CB LEU D 567 " pdb=" CD1 LEU D 567 " pdb=" CD2 LEU D 567 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU B 397 " pdb=" CB LEU B 397 " pdb=" CD1 LEU B 397 " pdb=" CD2 LEU B 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 4821 not shown) Planarity restraints: 5316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 373 " -0.022 2.00e-02 2.50e+03 2.11e-02 7.79e+00 pdb=" CG PHE B 373 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 373 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 373 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 373 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 373 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 373 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 611 " 0.181 9.50e-02 1.11e+02 8.16e-02 5.33e+00 pdb=" NE ARG C 611 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 611 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 611 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 611 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 467 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 468 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " -0.029 5.00e-02 4.00e+02 ... (remaining 5313 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7867 2.81 - 3.33: 30938 3.33 - 3.86: 50942 3.86 - 4.38: 54589 4.38 - 4.90: 95787 Nonbonded interactions: 240123 Sorted by model distance: nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.289 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.292 2.510 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.302 2.510 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.314 2.510 nonbonded pdb=" OE1 GLN A 831 " pdb="CA CA A2001 " model vdw 2.478 2.510 ... (remaining 240118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.830 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30956 Z= 0.159 Angle : 0.795 17.368 42100 Z= 0.387 Chirality : 0.039 0.305 4824 Planarity : 0.005 0.082 5316 Dihedral : 14.100 89.316 10812 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.81 % Allowed : 23.62 % Favored : 75.57 % 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: 1.43 (0.14), residues: 3900 helix: 1.84 (0.11), residues: 2484 sheet: -0.20 (0.37), residues: 216 loop : -0.71 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 611 TYR 0.021 0.001 TYR B 256 PHE 0.049 0.001 PHE B 373 TRP 0.029 0.001 TRP A 565 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (30948) covalent geometry : angle 0.79381 / 0.39 (42084) SS BOND : bond 0.00454 / 0.28 ( 8) SS BOND : angle 2.21286 / 1.30 ( 16) hydrogen bonds : bond 0.10014 / 7.24 ( 1902) hydrogen bonds : angle 4.71943 / 3.36 ( 5577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.799 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. REVERT: A 430 MET cc_start: 0.7840 (mtt) cc_final: 0.7380 (mpt) REVERT: A 440 PHE cc_start: 0.8971 (t80) cc_final: 0.8371 (m-80) REVERT: A 581 MET cc_start: 0.8126 (mmm) cc_final: 0.7557 (tpp) REVERT: A 601 ARG cc_start: 0.8576 (ptp-110) cc_final: 0.8032 (ptp-110) REVERT: A 644 ARG cc_start: 0.5418 (tpt170) cc_final: 0.3612 (ptm160) REVERT: A 670 ASP cc_start: 0.8487 (p0) cc_final: 0.8162 (m-30) REVERT: B 93 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8979 (tp) REVERT: B 372 GLU cc_start: 0.7863 (pp20) cc_final: 0.6689 (mp0) REVERT: B 430 MET cc_start: 0.7889 (mtt) cc_final: 0.7395 (mpt) REVERT: B 440 PHE cc_start: 0.9066 (t80) cc_final: 0.8707 (m-80) REVERT: B 581 MET cc_start: 0.8020 (mmm) cc_final: 0.7598 (tpp) REVERT: B 601 ARG cc_start: 0.8569 (ptp-110) cc_final: 0.8056 (ptp-110) REVERT: B 644 ARG cc_start: 0.5808 (tpt170) cc_final: 0.3798 (ptm160) REVERT: B 670 ASP cc_start: 0.8645 (p0) cc_final: 0.8362 (m-30) REVERT: B 690 ILE cc_start: 0.9028 (mp) cc_final: 0.8709 (mm) REVERT: B 1146 GLU cc_start: 0.8877 (tp30) cc_final: 0.8586 (tm-30) REVERT: C 429 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8595 (tm) REVERT: C 430 MET cc_start: 0.7627 (mmm) cc_final: 0.6955 (mpt) REVERT: C 454 PHE cc_start: 0.6469 (t80) cc_final: 0.6230 (t80) REVERT: C 581 MET cc_start: 0.7975 (mmm) cc_final: 0.7556 (tpp) REVERT: C 601 ARG cc_start: 0.8535 (ptp-110) cc_final: 0.8144 (ptp-110) REVERT: C 644 ARG cc_start: 0.5683 (tpt170) cc_final: 0.3642 (ptm160) REVERT: C 670 ASP cc_start: 0.8657 (p0) cc_final: 0.8314 (m-30) REVERT: C 990 HIS cc_start: 0.6979 (p-80) cc_final: 0.6230 (m170) REVERT: D 429 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8598 (tm) REVERT: D 430 MET cc_start: 0.7831 (mmm) cc_final: 0.7289 (mpt) REVERT: D 581 MET cc_start: 0.7952 (mmm) cc_final: 0.7624 (tpp) REVERT: D 601 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.8058 (ptp-110) REVERT: D 644 ARG cc_start: 0.5668 (tpt170) cc_final: 0.3659 (ptm160) REVERT: D 670 ASP cc_start: 0.8596 (p0) cc_final: 0.8253 (m-30) REVERT: D 935 PHE cc_start: 0.7680 (m-10) cc_final: 0.7231 (t80) REVERT: D 1146 GLU cc_start: 0.8953 (tp30) cc_final: 0.8561 (tm-30) outliers start: 24 outliers final: 14 residues processed: 255 average time/residue: 0.5653 time to fit residues: 172.7738 Evaluate side-chains 233 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 1083 SER Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 686 SER Chi-restraints excluded: chain D residue 1083 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 0.0010 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 573 GLN C 573 GLN ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.176598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100232 restraints weight = 62016.052| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.01 r_work: 0.3195 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30956 Z= 0.123 Angle : 0.615 14.237 42100 Z= 0.292 Chirality : 0.037 0.222 4824 Planarity : 0.005 0.045 5316 Dihedral : 4.249 59.711 4328 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 19.18 % Favored : 78.23 % 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: 1.58 (0.14), residues: 3900 helix: 1.98 (0.11), residues: 2492 sheet: -0.13 (0.36), residues: 216 loop : -0.72 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 611 TYR 0.008 0.001 TYR A1015 PHE 0.024 0.001 PHE C 373 TRP 0.013 0.001 TRP C 579 HIS 0.003 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (30948) covalent geometry : angle 0.61405 / 0.29 (42084) SS BOND : bond 0.00448 / 0.28 ( 8) SS BOND : angle 1.86274 / 1.08 ( 16) hydrogen bonds : bond 0.04914 / 3.38 ( 1902) hydrogen bonds : angle 4.29423 / 3.09 ( 5577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 252 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.5686 (OUTLIER) cc_final: 0.5446 (t) REVERT: A 435 ASN cc_start: 0.9088 (m-40) cc_final: 0.8754 (OUTLIER) REVERT: A 440 PHE cc_start: 0.8948 (t80) cc_final: 0.8599 (m-80) REVERT: A 601 ARG cc_start: 0.8468 (ptp-110) cc_final: 0.7848 (ptp-110) REVERT: A 644 ARG cc_start: 0.5103 (tpt170) cc_final: 0.3313 (ptm160) REVERT: A 670 ASP cc_start: 0.8315 (p0) cc_final: 0.7850 (m-30) REVERT: A 936 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 143 VAL cc_start: 0.5583 (OUTLIER) cc_final: 0.5342 (t) REVERT: B 440 PHE cc_start: 0.9048 (t80) cc_final: 0.8570 (m-80) REVERT: B 567 LEU cc_start: 0.7919 (mm) cc_final: 0.7717 (mm) REVERT: B 601 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.7857 (ptp-110) REVERT: B 622 MET cc_start: 0.7828 (ttm) cc_final: 0.7620 (ttp) REVERT: B 644 ARG cc_start: 0.5142 (tpt170) cc_final: 0.3392 (ptm160) REVERT: B 670 ASP cc_start: 0.8345 (p0) cc_final: 0.7945 (m-30) REVERT: B 690 ILE cc_start: 0.8797 (mp) cc_final: 0.8491 (mm) REVERT: B 1146 GLU cc_start: 0.8629 (tp30) cc_final: 0.8260 (tm-30) REVERT: C 143 VAL cc_start: 0.5651 (OUTLIER) cc_final: 0.5378 (t) REVERT: C 429 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8635 (tm) REVERT: C 601 ARG cc_start: 0.8326 (ptp-110) cc_final: 0.7858 (ptp-110) REVERT: C 625 ASP cc_start: 0.8521 (t0) cc_final: 0.8187 (p0) REVERT: C 644 ARG cc_start: 0.5072 (tpt170) cc_final: 0.3306 (ptm160) REVERT: C 670 ASP cc_start: 0.8363 (p0) cc_final: 0.7960 (m-30) REVERT: C 690 ILE cc_start: 0.8777 (mp) cc_final: 0.8435 (mm) REVERT: C 990 HIS cc_start: 0.7118 (p-80) cc_final: 0.6391 (m170) REVERT: C 1146 GLU cc_start: 0.8653 (tp30) cc_final: 0.8168 (tm-30) REVERT: D 299 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7068 (tm) REVERT: D 429 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8626 (tm) REVERT: D 430 MET cc_start: 0.7975 (mmm) cc_final: 0.7643 (mmm) REVERT: D 601 ARG cc_start: 0.8363 (ptp-110) cc_final: 0.7852 (ptp-110) REVERT: D 625 ASP cc_start: 0.8521 (t0) cc_final: 0.8149 (p0) REVERT: D 644 ARG cc_start: 0.5190 (tpt170) cc_final: 0.3312 (ptm160) REVERT: D 670 ASP cc_start: 0.8378 (p0) cc_final: 0.7912 (m-30) REVERT: D 935 PHE cc_start: 0.6935 (m-10) cc_final: 0.6418 (t80) REVERT: D 1146 GLU cc_start: 0.8665 (tp30) cc_final: 0.8234 (tm-30) outliers start: 77 outliers final: 24 residues processed: 318 average time/residue: 0.5225 time to fit residues: 200.2332 Evaluate side-chains 241 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 1085 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 989 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 110 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 377 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 chunk 104 optimal weight: 50.0000 chunk 217 optimal weight: 30.0000 chunk 239 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1017 ASN B1017 ASN C1017 ASN D 573 GLN D1017 ASN D1131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.176173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099703 restraints weight = 61846.251| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.99 r_work: 0.3191 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30956 Z= 0.116 Angle : 0.602 14.524 42100 Z= 0.285 Chirality : 0.037 0.152 4824 Planarity : 0.004 0.043 5316 Dihedral : 3.964 59.911 4309 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.13 % Allowed : 18.57 % Favored : 78.30 % 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: 1.66 (0.14), residues: 3900 helix: 2.04 (0.11), residues: 2488 sheet: -0.15 (0.36), residues: 216 loop : -0.69 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1119 TYR 0.008 0.001 TYR A1015 PHE 0.031 0.001 PHE B 373 TRP 0.009 0.001 TRP C 565 HIS 0.003 0.001 HIS B1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (30948) covalent geometry : angle 0.60174 / 0.28 (42084) SS BOND : bond 0.00376 / 0.23 ( 8) SS BOND : angle 1.55828 / 0.90 ( 16) hydrogen bonds : bond 0.04588 / 3.14 ( 1902) hydrogen bonds : angle 4.19537 / 3.02 ( 5577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 243 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.5853 (OUTLIER) cc_final: 0.5605 (t) REVERT: A 440 PHE cc_start: 0.9063 (t80) cc_final: 0.8576 (m-80) REVERT: A 581 MET cc_start: 0.8035 (mmm) cc_final: 0.7621 (tpp) REVERT: A 601 ARG cc_start: 0.8478 (ptp-110) cc_final: 0.7827 (ptp-110) REVERT: A 644 ARG cc_start: 0.5187 (tpt170) cc_final: 0.3345 (ptm160) REVERT: A 670 ASP cc_start: 0.8317 (p0) cc_final: 0.7896 (m-30) REVERT: A 690 ILE cc_start: 0.8809 (mp) cc_final: 0.8476 (mm) REVERT: A 804 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8069 (t70) REVERT: A 936 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: B 143 VAL cc_start: 0.5660 (OUTLIER) cc_final: 0.5405 (t) REVERT: B 299 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6370 (tm) REVERT: B 435 ASN cc_start: 0.9052 (m-40) cc_final: 0.8728 (p0) REVERT: B 440 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: B 567 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7655 (mm) REVERT: B 601 ARG cc_start: 0.8458 (ptp-110) cc_final: 0.7912 (ptp-110) REVERT: B 644 ARG cc_start: 0.5070 (tpt170) cc_final: 0.3289 (ptm160) REVERT: B 670 ASP cc_start: 0.8358 (p0) cc_final: 0.8007 (m-30) REVERT: B 690 ILE cc_start: 0.8783 (mp) cc_final: 0.8481 (mm) REVERT: B 936 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: B 1146 GLU cc_start: 0.8661 (tp30) cc_final: 0.8256 (tm-30) REVERT: C 143 VAL cc_start: 0.5541 (OUTLIER) cc_final: 0.5266 (t) REVERT: C 299 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6934 (tm) REVERT: C 429 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8626 (tm) REVERT: C 435 ASN cc_start: 0.9018 (m-40) cc_final: 0.8810 (p0) REVERT: C 601 ARG cc_start: 0.8331 (ptp-110) cc_final: 0.7811 (ptp-110) REVERT: C 625 ASP cc_start: 0.8547 (t0) cc_final: 0.8181 (p0) REVERT: C 644 ARG cc_start: 0.5100 (tpt170) cc_final: 0.3332 (ptm160) REVERT: C 670 ASP cc_start: 0.8352 (p0) cc_final: 0.7995 (m-30) REVERT: C 690 ILE cc_start: 0.8781 (mp) cc_final: 0.8431 (mm) REVERT: C 784 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7161 (ttm) REVERT: C 936 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: C 990 HIS cc_start: 0.7300 (p-80) cc_final: 0.6581 (m170) REVERT: C 1146 GLU cc_start: 0.8728 (tp30) cc_final: 0.8243 (tm-30) REVERT: D 175 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7933 (mpt) REVERT: D 299 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7090 (tm) REVERT: D 429 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8624 (tm) REVERT: D 430 MET cc_start: 0.8046 (mmm) cc_final: 0.7799 (mmm) REVERT: D 601 ARG cc_start: 0.8344 (ptp-110) cc_final: 0.7803 (ptp-110) REVERT: D 625 ASP cc_start: 0.8539 (t0) cc_final: 0.8208 (p0) REVERT: D 644 ARG cc_start: 0.5168 (tpt170) cc_final: 0.3369 (ptm160) REVERT: D 670 ASP cc_start: 0.8326 (p0) cc_final: 0.7920 (m-30) REVERT: D 935 PHE cc_start: 0.6924 (m-10) cc_final: 0.6438 (t80) REVERT: D 936 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: D 1146 GLU cc_start: 0.8686 (tp30) cc_final: 0.8256 (tm-30) outliers start: 93 outliers final: 28 residues processed: 326 average time/residue: 0.4997 time to fit residues: 198.5007 Evaluate side-chains 266 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 989 GLU Chi-restraints excluded: chain D residue 1087 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 147 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 211 optimal weight: 40.0000 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 chunk 371 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.168353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089038 restraints weight = 59769.824| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.94 r_work: 0.3016 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 30956 Z= 0.212 Angle : 0.687 11.150 42100 Z= 0.345 Chirality : 0.040 0.212 4824 Planarity : 0.005 0.047 5316 Dihedral : 4.304 59.861 4307 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 4.00 % Allowed : 18.64 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.38 (0.14), residues: 3900 helix: 1.81 (0.11), residues: 2468 sheet: -0.12 (0.35), residues: 220 loop : -0.74 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1166 TYR 0.012 0.001 TYR A1015 PHE 0.023 0.002 PHE D 373 TRP 0.016 0.001 TRP A 565 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (30948) covalent geometry : angle 0.68015 / 0.34 (42084) SS BOND : bond 0.00642 / 0.40 ( 8) SS BOND : angle 4.89662 / 2.83 ( 16) hydrogen bonds : bond 0.06867 / 4.69 ( 1902) hydrogen bonds : angle 4.46053 / 3.22 ( 5577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 253 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: A 643 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8615 (mt) REVERT: A 644 ARG cc_start: 0.5395 (tpt170) cc_final: 0.3532 (ppt170) REVERT: A 670 ASP cc_start: 0.8527 (p0) cc_final: 0.8292 (m-30) REVERT: A 690 ILE cc_start: 0.8865 (mp) cc_final: 0.8575 (mm) REVERT: A 936 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: B 140 ARG cc_start: 0.6813 (mtp85) cc_final: 0.6227 (mtp85) REVERT: B 143 VAL cc_start: 0.5943 (OUTLIER) cc_final: 0.5682 (t) REVERT: B 440 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: B 567 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8069 (mm) REVERT: B 581 MET cc_start: 0.8479 (mmm) cc_final: 0.8074 (tpp) REVERT: B 644 ARG cc_start: 0.5217 (tpt170) cc_final: 0.3560 (ptm160) REVERT: B 690 ILE cc_start: 0.8850 (mp) cc_final: 0.8580 (mm) REVERT: B 936 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: B 1120 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8045 (tmmm) REVERT: B 1134 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 1146 GLU cc_start: 0.8870 (tp30) cc_final: 0.8363 (tm-30) REVERT: C 143 VAL cc_start: 0.6078 (OUTLIER) cc_final: 0.5809 (t) REVERT: C 299 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7022 (tm) REVERT: C 429 LEU cc_start: 0.8892 (mt) cc_final: 0.8590 (tm) REVERT: C 435 ASN cc_start: 0.9132 (m-40) cc_final: 0.8865 (p0) REVERT: C 581 MET cc_start: 0.8438 (mmm) cc_final: 0.8099 (tpp) REVERT: C 643 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8631 (mt) REVERT: C 644 ARG cc_start: 0.5342 (tpt170) cc_final: 0.3548 (ptm160) REVERT: C 670 ASP cc_start: 0.8556 (p0) cc_final: 0.8349 (m-30) REVERT: C 690 ILE cc_start: 0.8878 (mp) cc_final: 0.8573 (mm) REVERT: C 936 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: C 990 HIS cc_start: 0.7798 (p-80) cc_final: 0.7069 (m170) REVERT: C 1130 GLU cc_start: 0.8215 (pp20) cc_final: 0.7925 (pp20) REVERT: C 1146 GLU cc_start: 0.8888 (tp30) cc_final: 0.8365 (tm-30) REVERT: D 175 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8030 (mpp) REVERT: D 429 LEU cc_start: 0.8865 (mt) cc_final: 0.8652 (tm) REVERT: D 430 MET cc_start: 0.8362 (mmm) cc_final: 0.8000 (mmm) REVERT: D 567 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8031 (mm) REVERT: D 581 MET cc_start: 0.8434 (mmm) cc_final: 0.8066 (tpp) REVERT: D 644 ARG cc_start: 0.5386 (tpt170) cc_final: 0.3521 (ptm160) REVERT: D 670 ASP cc_start: 0.8531 (p0) cc_final: 0.8323 (m-30) REVERT: D 702 LEU cc_start: 0.8551 (mp) cc_final: 0.8033 (tt) REVERT: D 935 PHE cc_start: 0.7288 (m-10) cc_final: 0.6475 (t80) REVERT: D 936 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: D 1130 GLU cc_start: 0.8535 (pt0) cc_final: 0.8290 (pp20) REVERT: D 1146 GLU cc_start: 0.8886 (tp30) cc_final: 0.8381 (tm-30) outliers start: 119 outliers final: 41 residues processed: 356 average time/residue: 0.4771 time to fit residues: 207.9391 Evaluate side-chains 278 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1120 LYS Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 989 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 152 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 147 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 369 optimal weight: 0.7980 chunk 394 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 573 GLN B 678 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 GLN C1017 ASN C1164 HIS ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.164024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084526 restraints weight = 60605.365| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.00 r_work: 0.2912 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 30956 Z= 0.247 Angle : 0.738 13.938 42100 Z= 0.366 Chirality : 0.042 0.344 4824 Planarity : 0.005 0.049 5316 Dihedral : 4.283 59.436 4303 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 4.41 % Allowed : 18.98 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.09 (0.14), residues: 3900 helix: 1.52 (0.11), residues: 2472 sheet: -0.17 (0.36), residues: 212 loop : -0.72 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 140 TYR 0.018 0.001 TYR B 256 PHE 0.029 0.002 PHE B 710 TRP 0.017 0.001 TRP A 565 HIS 0.009 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (30948) covalent geometry : angle 0.73013 / 0.36 (42084) SS BOND : bond 0.01378 / 0.84 ( 8) SS BOND : angle 5.67554 / 3.26 ( 16) hydrogen bonds : bond 0.07197 / 4.94 ( 1902) hydrogen bonds : angle 4.61257 / 3.33 ( 5577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 273 time to evaluate : 0.689 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 378 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6007 (mt) REVERT: A 440 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: A 567 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8330 (mm) REVERT: A 581 MET cc_start: 0.8819 (mmm) cc_final: 0.8380 (tpp) REVERT: A 644 ARG cc_start: 0.5269 (tpt170) cc_final: 0.3666 (ptm160) REVERT: A 690 ILE cc_start: 0.8743 (mp) cc_final: 0.8445 (mm) REVERT: A 702 LEU cc_start: 0.8728 (mp) cc_final: 0.8251 (tt) REVERT: A 936 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8184 (m-80) REVERT: B 140 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7132 (mtp85) REVERT: B 378 LEU cc_start: 0.6250 (mt) cc_final: 0.5902 (mt) REVERT: B 430 MET cc_start: 0.8334 (mmm) cc_final: 0.8036 (mmm) REVERT: B 440 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: B 567 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (mm) REVERT: B 581 MET cc_start: 0.8807 (mmm) cc_final: 0.8277 (tpp) REVERT: B 644 ARG cc_start: 0.5017 (tpt170) cc_final: 0.3371 (ptm160) REVERT: B 690 ILE cc_start: 0.8789 (mp) cc_final: 0.8529 (mm) REVERT: B 702 LEU cc_start: 0.8747 (mp) cc_final: 0.8280 (tt) REVERT: B 936 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: B 1146 GLU cc_start: 0.8923 (tp30) cc_final: 0.8326 (tm-30) REVERT: C 140 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7404 (mtp85) REVERT: C 299 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7384 (tm) REVERT: C 429 LEU cc_start: 0.8995 (mt) cc_final: 0.8628 (tm) REVERT: C 440 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: C 567 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8250 (mm) REVERT: C 581 MET cc_start: 0.8858 (mmm) cc_final: 0.8428 (tpp) REVERT: C 644 ARG cc_start: 0.5334 (tpt170) cc_final: 0.3708 (ptm160) REVERT: C 686 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8600 (t) REVERT: C 690 ILE cc_start: 0.8794 (mp) cc_final: 0.8498 (mm) REVERT: C 936 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: C 988 MET cc_start: 0.9082 (ptt) cc_final: 0.8595 (ptt) REVERT: C 990 HIS cc_start: 0.7978 (p-80) cc_final: 0.7381 (m90) REVERT: C 1138 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7894 (tmm-80) REVERT: C 1146 GLU cc_start: 0.8929 (tp30) cc_final: 0.8312 (tm-30) REVERT: D 175 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8036 (mpp) REVERT: D 429 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8607 (tm) REVERT: D 430 MET cc_start: 0.8513 (mmm) cc_final: 0.8198 (mmm) REVERT: D 440 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8964 (m-80) REVERT: D 567 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8197 (mm) REVERT: D 581 MET cc_start: 0.8823 (mmm) cc_final: 0.8396 (tpp) REVERT: D 644 ARG cc_start: 0.5329 (tpt170) cc_final: 0.3619 (ptm160) REVERT: D 702 LEU cc_start: 0.8672 (mp) cc_final: 0.8205 (tt) REVERT: D 935 PHE cc_start: 0.7211 (m-10) cc_final: 0.6270 (t80) REVERT: D 936 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: D 989 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: D 1146 GLU cc_start: 0.8937 (tp30) cc_final: 0.8411 (tm-30) outliers start: 131 outliers final: 41 residues processed: 385 average time/residue: 0.4908 time to fit residues: 230.4827 Evaluate side-chains 284 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 989 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 175 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 217 optimal weight: 0.4980 chunk 227 optimal weight: 40.0000 chunk 312 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN B 505 HIS ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C1017 ASN ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.162128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.082987 restraints weight = 60407.334| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.05 r_work: 0.2891 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 30956 Z= 0.233 Angle : 0.723 12.230 42100 Z= 0.355 Chirality : 0.041 0.366 4824 Planarity : 0.005 0.075 5316 Dihedral : 4.261 59.154 4303 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 3.43 % Allowed : 20.69 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.15 (0.14), residues: 3900 helix: 1.62 (0.11), residues: 2440 sheet: -0.26 (0.36), residues: 212 loop : -0.71 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 144 TYR 0.032 0.001 TYR B 464 PHE 0.020 0.002 PHE D 440 TRP 0.017 0.001 TRP A 565 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 (30948) covalent geometry : angle 0.71431 / 0.35 (42084) SS BOND : bond 0.00975 / 0.59 ( 8) SS BOND : angle 5.66958 / 3.25 ( 16) hydrogen bonds : bond 0.07162 / 4.91 ( 1902) hydrogen bonds : angle 4.57145 / 3.30 ( 5577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 246 time to evaluate : 1.146 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 373 PHE cc_start: 0.7000 (t80) cc_final: 0.6582 (t80) REVERT: A 430 MET cc_start: 0.8504 (mmm) cc_final: 0.8208 (mmm) REVERT: A 440 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: A 581 MET cc_start: 0.8835 (mmm) cc_final: 0.8603 (tpp) REVERT: A 644 ARG cc_start: 0.5315 (tpt170) cc_final: 0.3627 (ptm160) REVERT: A 690 ILE cc_start: 0.8779 (mp) cc_final: 0.8483 (mm) REVERT: A 936 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: A 955 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8122 (tpp-160) REVERT: A 989 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: B 140 ARG cc_start: 0.7368 (mtp85) cc_final: 0.6406 (mtp85) REVERT: B 430 MET cc_start: 0.8532 (mmm) cc_final: 0.8097 (mmm) REVERT: B 440 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8864 (m-80) REVERT: B 505 HIS cc_start: 0.8620 (m-70) cc_final: 0.8312 (m90) REVERT: B 567 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8495 (mm) REVERT: B 581 MET cc_start: 0.8720 (mmm) cc_final: 0.8515 (tpp) REVERT: B 644 ARG cc_start: 0.4947 (tpt170) cc_final: 0.3376 (ptm160) REVERT: B 690 ILE cc_start: 0.8818 (mp) cc_final: 0.8546 (mm) REVERT: B 702 LEU cc_start: 0.8746 (mp) cc_final: 0.8283 (tt) REVERT: B 936 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: B 1146 GLU cc_start: 0.8921 (tp30) cc_final: 0.8256 (tm-30) REVERT: C 135 GLN cc_start: 0.8358 (tt0) cc_final: 0.7682 (tm-30) REVERT: C 361 LEU cc_start: 0.6144 (pt) cc_final: 0.5758 (mp) REVERT: C 429 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8694 (tm) REVERT: C 567 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8432 (mm) REVERT: C 644 ARG cc_start: 0.5437 (tpt170) cc_final: 0.3544 (ptm160) REVERT: C 686 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8641 (t) REVERT: C 690 ILE cc_start: 0.8771 (mp) cc_final: 0.8493 (mm) REVERT: C 936 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: C 988 MET cc_start: 0.8921 (ptt) cc_final: 0.8510 (ptt) REVERT: C 990 HIS cc_start: 0.7887 (p-80) cc_final: 0.7277 (m90) REVERT: C 1146 GLU cc_start: 0.8966 (tp30) cc_final: 0.8272 (tm-30) REVERT: D 135 GLN cc_start: 0.8342 (tt0) cc_final: 0.7734 (tm-30) REVERT: D 175 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.8003 (mpp) REVERT: D 430 MET cc_start: 0.8634 (mmm) cc_final: 0.8364 (mmm) REVERT: D 567 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8434 (mm) REVERT: D 644 ARG cc_start: 0.5330 (tpt170) cc_final: 0.3619 (ptm160) REVERT: D 702 LEU cc_start: 0.8733 (mp) cc_final: 0.8241 (tt) REVERT: D 935 PHE cc_start: 0.7241 (m-10) cc_final: 0.6317 (t80) REVERT: D 936 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: D 955 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8112 (tpp-160) REVERT: D 989 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: D 1146 GLU cc_start: 0.8984 (tp30) cc_final: 0.8354 (tm-30) outliers start: 102 outliers final: 43 residues processed: 330 average time/residue: 0.5030 time to fit residues: 202.2013 Evaluate side-chains 277 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 955 ARG Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 989 GLU Chi-restraints excluded: chain D residue 1087 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 58 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 101 optimal weight: 0.0470 chunk 388 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 132 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 573 GLN C1017 ASN D 573 GLN D1131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.164661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087071 restraints weight = 60903.069| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.01 r_work: 0.2966 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 30956 Z= 0.136 Angle : 0.676 15.007 42100 Z= 0.323 Chirality : 0.038 0.363 4824 Planarity : 0.005 0.055 5316 Dihedral : 4.175 59.106 4303 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.86 % Allowed : 21.77 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.46 (0.14), residues: 3900 helix: 1.87 (0.11), residues: 2468 sheet: -0.23 (0.36), residues: 212 loop : -0.66 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 144 TYR 0.018 0.001 TYR D 464 PHE 0.020 0.001 PHE C 627 TRP 0.013 0.001 TRP D 420 HIS 0.003 0.000 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (30948) covalent geometry : angle 0.66901 / 0.32 (42084) SS BOND : bond 0.00943 / 0.57 ( 8) SS BOND : angle 5.15538 / 3.01 ( 16) hydrogen bonds : bond 0.05405 / 3.71 ( 1902) hydrogen bonds : angle 4.29347 / 3.10 ( 5577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 257 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8333 (tt0) cc_final: 0.7750 (tm-30) REVERT: A 373 PHE cc_start: 0.7120 (t80) cc_final: 0.6625 (t80) REVERT: A 430 MET cc_start: 0.8600 (mmm) cc_final: 0.8273 (mmm) REVERT: A 440 PHE cc_start: 0.9144 (t80) cc_final: 0.8756 (m-80) REVERT: A 567 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8501 (mm) REVERT: A 581 MET cc_start: 0.8745 (mmm) cc_final: 0.7881 (mpp) REVERT: A 644 ARG cc_start: 0.5089 (tpt170) cc_final: 0.3470 (ppt170) REVERT: A 690 ILE cc_start: 0.8730 (mp) cc_final: 0.8420 (mm) REVERT: A 702 LEU cc_start: 0.8684 (mp) cc_final: 0.8213 (tt) REVERT: A 936 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: A 989 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: B 440 PHE cc_start: 0.9216 (t80) cc_final: 0.8890 (m-80) REVERT: B 505 HIS cc_start: 0.8671 (m-70) cc_final: 0.8407 (m90) REVERT: B 567 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8541 (mm) REVERT: B 581 MET cc_start: 0.8718 (mmm) cc_final: 0.8250 (tpp) REVERT: B 644 ARG cc_start: 0.5099 (tpt170) cc_final: 0.3387 (ppt170) REVERT: B 690 ILE cc_start: 0.8757 (mp) cc_final: 0.8462 (mm) REVERT: B 702 LEU cc_start: 0.8710 (mp) cc_final: 0.8290 (tt) REVERT: B 936 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: B 1146 GLU cc_start: 0.8890 (tp30) cc_final: 0.8209 (tm-30) REVERT: B 1153 GLN cc_start: 0.9004 (tm130) cc_final: 0.8765 (tm-30) REVERT: C 93 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9052 (mt) REVERT: C 135 GLN cc_start: 0.8405 (tt0) cc_final: 0.7742 (tm-30) REVERT: C 361 LEU cc_start: 0.6116 (pt) cc_final: 0.5703 (mp) REVERT: C 429 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8751 (tm) REVERT: C 567 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8493 (mm) REVERT: C 581 MET cc_start: 0.8487 (tpp) cc_final: 0.8196 (tpp) REVERT: C 644 ARG cc_start: 0.5092 (tpt170) cc_final: 0.3554 (ptm160) REVERT: C 686 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8522 (t) REVERT: C 690 ILE cc_start: 0.8764 (mp) cc_final: 0.8464 (mm) REVERT: C 702 LEU cc_start: 0.8640 (mp) cc_final: 0.8127 (tt) REVERT: C 936 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: C 988 MET cc_start: 0.8871 (ptt) cc_final: 0.8583 (ptt) REVERT: C 990 HIS cc_start: 0.7836 (p-80) cc_final: 0.7187 (m90) REVERT: C 1146 GLU cc_start: 0.8938 (tp30) cc_final: 0.8214 (tm-30) REVERT: D 93 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9054 (mt) REVERT: D 135 GLN cc_start: 0.8318 (tt0) cc_final: 0.7719 (tm-30) REVERT: D 175 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7980 (mpt) REVERT: D 567 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8355 (mm) REVERT: D 581 MET cc_start: 0.8447 (tpp) cc_final: 0.8181 (tpp) REVERT: D 644 ARG cc_start: 0.5100 (tpt170) cc_final: 0.3579 (ppt170) REVERT: D 702 LEU cc_start: 0.8688 (mp) cc_final: 0.8229 (tt) REVERT: D 935 PHE cc_start: 0.7058 (m-10) cc_final: 0.6183 (t80) REVERT: D 936 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: D 989 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: D 1146 GLU cc_start: 0.8945 (tp30) cc_final: 0.8313 (tm-30) outliers start: 85 outliers final: 40 residues processed: 329 average time/residue: 0.5222 time to fit residues: 207.3583 Evaluate side-chains 278 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 GLU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 989 GLU Chi-restraints excluded: chain D residue 1087 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 326 optimal weight: 30.0000 chunk 294 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 118 optimal weight: 50.0000 chunk 193 optimal weight: 0.8980 chunk 300 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 311 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS C 475 ASN C 505 HIS ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.158002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.079205 restraints weight = 60598.975| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.93 r_work: 0.2829 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 30956 Z= 0.308 Angle : 0.791 13.121 42100 Z= 0.396 Chirality : 0.044 0.312 4824 Planarity : 0.006 0.055 5316 Dihedral : 4.395 59.554 4303 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.20 % Allowed : 22.41 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.95 (0.14), residues: 3900 helix: 1.44 (0.10), residues: 2444 sheet: -0.33 (0.35), residues: 212 loop : -0.75 (0.19), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 144 TYR 0.017 0.002 TYR B 256 PHE 0.018 0.002 PHE B 783 TRP 0.020 0.002 TRP C 680 HIS 0.007 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.31 (30948) covalent geometry : angle 0.78464 / 0.39 (42084) SS BOND : bond 0.00997 / 0.60 ( 8) SS BOND : angle 5.21513 / 3.07 ( 16) hydrogen bonds : bond 0.08544 / 5.85 ( 1902) hydrogen bonds : angle 4.81573 / 3.47 ( 5577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 265 time to evaluate : 0.727 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 135 GLN cc_start: 0.8460 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 373 PHE cc_start: 0.7385 (t80) cc_final: 0.6847 (t80) REVERT: A 440 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: A 567 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 581 MET cc_start: 0.8925 (mmm) cc_final: 0.8032 (mpp) REVERT: A 644 ARG cc_start: 0.5288 (tpt170) cc_final: 0.3520 (ptm160) REVERT: A 690 ILE cc_start: 0.8748 (mp) cc_final: 0.8502 (mm) REVERT: A 935 PHE cc_start: 0.7804 (t80) cc_final: 0.7595 (t80) REVERT: A 936 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: A 955 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8149 (tpp-160) REVERT: B 135 GLN cc_start: 0.8412 (tt0) cc_final: 0.7742 (tm-30) REVERT: B 430 MET cc_start: 0.8430 (mmm) cc_final: 0.8130 (mmm) REVERT: B 440 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8988 (m-80) REVERT: B 444 LEU cc_start: 0.9312 (mt) cc_final: 0.9061 (mt) REVERT: B 567 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8512 (mm) REVERT: B 581 MET cc_start: 0.8806 (mmm) cc_final: 0.8486 (tpp) REVERT: B 644 ARG cc_start: 0.5084 (tpt170) cc_final: 0.3445 (ptm160) REVERT: B 690 ILE cc_start: 0.8758 (mp) cc_final: 0.8507 (mm) REVERT: B 936 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: B 989 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: B 1146 GLU cc_start: 0.8889 (tp30) cc_final: 0.8164 (tm-30) REVERT: C 135 GLN cc_start: 0.8525 (tt0) cc_final: 0.7923 (tm-30) REVERT: C 361 LEU cc_start: 0.6657 (pt) cc_final: 0.6274 (mp) REVERT: C 377 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (t) REVERT: C 429 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8561 (tm) REVERT: C 567 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8593 (mm) REVERT: C 644 ARG cc_start: 0.5321 (tpt170) cc_final: 0.3522 (ptm160) REVERT: C 686 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8777 (t) REVERT: C 690 ILE cc_start: 0.8754 (mp) cc_final: 0.8507 (mm) REVERT: C 936 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: D 135 GLN cc_start: 0.8463 (tt0) cc_final: 0.7890 (tm-30) REVERT: D 175 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7926 (mpp) REVERT: D 430 MET cc_start: 0.8685 (mmm) cc_final: 0.8273 (mmm) REVERT: D 440 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.9014 (t80) REVERT: D 444 LEU cc_start: 0.9324 (mt) cc_final: 0.8969 (mt) REVERT: D 567 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8510 (mm) REVERT: D 644 ARG cc_start: 0.5421 (tpt170) cc_final: 0.3675 (ptm160) REVERT: D 702 LEU cc_start: 0.8736 (mp) cc_final: 0.8217 (tt) REVERT: D 935 PHE cc_start: 0.7151 (m-10) cc_final: 0.6173 (t80) REVERT: D 936 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: D 955 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8157 (tpp-160) REVERT: D 989 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: D 1146 GLU cc_start: 0.8957 (tp30) cc_final: 0.8230 (tm-30) outliers start: 95 outliers final: 29 residues processed: 348 average time/residue: 0.5237 time to fit residues: 220.7624 Evaluate side-chains 271 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 955 ARG Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 989 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 158 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 277 optimal weight: 0.9990 chunk 128 optimal weight: 40.0000 chunk 149 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.161289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.084280 restraints weight = 60205.973| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.83 r_work: 0.2931 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 30956 Z= 0.148 Angle : 0.731 13.161 42100 Z= 0.350 Chirality : 0.040 0.357 4824 Planarity : 0.005 0.086 5316 Dihedral : 4.299 59.371 4303 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.88 % Allowed : 24.50 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.35 (0.14), residues: 3900 helix: 1.76 (0.11), residues: 2452 sheet: -0.39 (0.35), residues: 212 loop : -0.58 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1141 TYR 0.021 0.001 TYR C 256 PHE 0.020 0.001 PHE C 627 TRP 0.014 0.001 TRP A 420 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (30948) covalent geometry : angle 0.72402 / 0.35 (42084) SS BOND : bond 0.00936 / 0.56 ( 8) SS BOND : angle 5.14766 / 3.00 ( 16) hydrogen bonds : bond 0.05836 / 4.01 ( 1902) hydrogen bonds : angle 4.44388 / 3.20 ( 5577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 135 GLN cc_start: 0.8465 (tt0) cc_final: 0.7827 (tm-30) REVERT: A 430 MET cc_start: 0.8607 (mmm) cc_final: 0.8311 (mmm) REVERT: A 440 PHE cc_start: 0.9100 (t80) cc_final: 0.8797 (m-80) REVERT: A 567 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8539 (mm) REVERT: A 644 ARG cc_start: 0.4990 (tpt170) cc_final: 0.3376 (ptm160) REVERT: A 690 ILE cc_start: 0.8743 (mp) cc_final: 0.8417 (mm) REVERT: A 702 LEU cc_start: 0.8670 (mp) cc_final: 0.8263 (tt) REVERT: A 936 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: A 1141 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7826 (tmm-80) REVERT: A 1153 GLN cc_start: 0.9049 (tm130) cc_final: 0.8823 (tm-30) REVERT: B 135 GLN cc_start: 0.8418 (tt0) cc_final: 0.7725 (tm-30) REVERT: B 440 PHE cc_start: 0.9155 (t80) cc_final: 0.8913 (m-80) REVERT: B 567 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8628 (mm) REVERT: B 644 ARG cc_start: 0.5111 (tpt170) cc_final: 0.3390 (ppt170) REVERT: B 690 ILE cc_start: 0.8765 (mp) cc_final: 0.8472 (mm) REVERT: B 702 LEU cc_start: 0.8735 (mp) cc_final: 0.8275 (tt) REVERT: B 936 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: B 989 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: B 1141 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7799 (ttp80) REVERT: B 1146 GLU cc_start: 0.8863 (tp30) cc_final: 0.8169 (tm-30) REVERT: C 135 GLN cc_start: 0.8540 (tt0) cc_final: 0.7906 (tm-30) REVERT: C 361 LEU cc_start: 0.6581 (pt) cc_final: 0.6131 (mp) REVERT: C 430 MET cc_start: 0.8641 (mmm) cc_final: 0.8192 (mmm) REVERT: C 567 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8490 (mm) REVERT: C 644 ARG cc_start: 0.5018 (tpt170) cc_final: 0.3534 (ptm160) REVERT: C 686 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8629 (t) REVERT: C 690 ILE cc_start: 0.8677 (mp) cc_final: 0.8372 (mm) REVERT: C 702 LEU cc_start: 0.8680 (mp) cc_final: 0.8174 (tt) REVERT: C 936 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: D 135 GLN cc_start: 0.8385 (tt0) cc_final: 0.7775 (tm-30) REVERT: D 175 MET cc_start: 0.8304 (mpp) cc_final: 0.7962 (mpt) REVERT: D 567 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8538 (mm) REVERT: D 644 ARG cc_start: 0.4901 (tpt170) cc_final: 0.3549 (ptm160) REVERT: D 702 LEU cc_start: 0.8656 (mp) cc_final: 0.8205 (tt) REVERT: D 935 PHE cc_start: 0.7104 (m-10) cc_final: 0.6206 (t80) REVERT: D 936 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: D 989 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: D 1141 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7831 (ttp80) REVERT: D 1146 GLU cc_start: 0.8930 (tp30) cc_final: 0.8195 (tm-30) REVERT: D 1153 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8821 (pp30) outliers start: 56 outliers final: 26 residues processed: 314 average time/residue: 0.6023 time to fit residues: 226.6708 Evaluate side-chains 278 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 955 ARG Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 989 GLU Chi-restraints excluded: chain D residue 995 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 242 optimal weight: 0.0870 chunk 302 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 313 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 381 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 340 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 overall best weight: 2.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.158807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081451 restraints weight = 59896.108| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.89 r_work: 0.2873 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30956 Z= 0.197 Angle : 0.753 12.760 42100 Z= 0.364 Chirality : 0.041 0.272 4824 Planarity : 0.005 0.072 5316 Dihedral : 4.252 59.406 4303 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 1.78 % Allowed : 25.00 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.14), residues: 3900 helix: 1.71 (0.11), residues: 2448 sheet: -0.24 (0.36), residues: 204 loop : -0.69 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C1141 TYR 0.019 0.001 TYR D 256 PHE 0.020 0.002 PHE C 373 TRP 0.022 0.001 TRP D 565 HIS 0.006 0.001 HIS C 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (30948) covalent geometry : angle 0.74544 / 0.36 (42084) SS BOND : bond 0.01213 / 0.74 ( 8) SS BOND : angle 5.40335 / 3.17 ( 16) hydrogen bonds : bond 0.06679 / 4.57 ( 1902) hydrogen bonds : angle 4.55335 / 3.28 ( 5577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 135 GLN cc_start: 0.8538 (tt0) cc_final: 0.7927 (tm-30) REVERT: A 373 PHE cc_start: 0.7593 (t80) cc_final: 0.7200 (t80) REVERT: A 440 PHE cc_start: 0.9058 (t80) cc_final: 0.8820 (m-80) REVERT: A 567 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8508 (mm) REVERT: A 581 MET cc_start: 0.8870 (mmm) cc_final: 0.8384 (mmm) REVERT: A 644 ARG cc_start: 0.5191 (tpt170) cc_final: 0.3580 (ptm160) REVERT: A 690 ILE cc_start: 0.8732 (mp) cc_final: 0.8444 (mm) REVERT: A 702 LEU cc_start: 0.8695 (mp) cc_final: 0.8199 (tt) REVERT: A 936 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: B 135 GLN cc_start: 0.8433 (tt0) cc_final: 0.7772 (tm-30) REVERT: B 440 PHE cc_start: 0.9146 (t80) cc_final: 0.8923 (m-80) REVERT: B 567 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8632 (mm) REVERT: B 644 ARG cc_start: 0.5084 (tpt170) cc_final: 0.3407 (ptm160) REVERT: B 690 ILE cc_start: 0.8786 (mp) cc_final: 0.8506 (mm) REVERT: B 702 LEU cc_start: 0.8721 (mp) cc_final: 0.8232 (tt) REVERT: B 936 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: B 989 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: B 1146 GLU cc_start: 0.8866 (tp30) cc_final: 0.8188 (tm-30) REVERT: C 135 GLN cc_start: 0.8561 (tt0) cc_final: 0.7917 (tm-30) REVERT: C 361 LEU cc_start: 0.6729 (pt) cc_final: 0.6288 (mp) REVERT: C 567 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8516 (mm) REVERT: C 644 ARG cc_start: 0.5219 (tpt170) cc_final: 0.3683 (ptm160) REVERT: C 686 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8660 (t) REVERT: C 690 ILE cc_start: 0.8699 (mp) cc_final: 0.8421 (mm) REVERT: C 702 LEU cc_start: 0.8718 (mp) cc_final: 0.8208 (tt) REVERT: C 936 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: D 135 GLN cc_start: 0.8603 (tt0) cc_final: 0.7989 (tm-30) REVERT: D 171 ARG cc_start: 0.9029 (ppt90) cc_final: 0.8799 (ppt90) REVERT: D 175 MET cc_start: 0.8321 (mpp) cc_final: 0.8053 (mpp) REVERT: D 567 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8509 (mm) REVERT: D 644 ARG cc_start: 0.5212 (tpt170) cc_final: 0.3632 (ptm160) REVERT: D 702 LEU cc_start: 0.8690 (mp) cc_final: 0.8227 (tt) REVERT: D 935 PHE cc_start: 0.7187 (m-10) cc_final: 0.6281 (t80) REVERT: D 936 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: D 1146 GLU cc_start: 0.8928 (tp30) cc_final: 0.8196 (tm-30) outliers start: 53 outliers final: 30 residues processed: 304 average time/residue: 0.5201 time to fit residues: 193.0563 Evaluate side-chains 286 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 955 ARG Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 989 GLU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 699 CYS Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain D residue 37 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 955 ARG Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 1087 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 141 optimal weight: 7.9990 chunk 2 optimal weight: 0.0050 chunk 346 optimal weight: 1.9990 chunk 104 optimal weight: 50.0000 chunk 74 optimal weight: 0.8980 chunk 375 optimal weight: 0.6980 chunk 316 optimal weight: 50.0000 chunk 372 optimal weight: 0.8980 chunk 333 optimal weight: 20.0000 chunk 103 optimal weight: 0.3980 chunk 238 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.162019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087664 restraints weight = 61050.341| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.87 r_work: 0.2927 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 30956 Z= 0.139 Angle : 0.746 15.119 42100 Z= 0.351 Chirality : 0.039 0.280 4824 Planarity : 0.005 0.077 5316 Dihedral : 4.243 59.150 4303 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.55 % Allowed : 25.37 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.51 (0.14), residues: 3900 helix: 1.90 (0.11), residues: 2452 sheet: -0.23 (0.35), residues: 204 loop : -0.59 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D1119 TYR 0.029 0.001 TYR C 256 PHE 0.019 0.001 PHE C 627 TRP 0.026 0.001 TRP D 565 HIS 0.004 0.001 HIS D 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (30948) covalent geometry : angle 0.73888 / 0.35 (42084) SS BOND : bond 0.00831 / 0.49 ( 8) SS BOND : angle 5.50683 / 3.20 ( 16) hydrogen bonds : bond 0.04913 / 3.38 ( 1902) hydrogen bonds : angle 4.35079 / 3.13 ( 5577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11523.64 seconds wall clock time: 195 minutes 56.39 seconds (11756.39 seconds total)