Starting phenix.real_space_refine on Sat Feb 7 08:11:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtc_48605/02_2026/9mtc_48605.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtc_48605/02_2026/9mtc_48605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mtc_48605/02_2026/9mtc_48605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtc_48605/02_2026/9mtc_48605.map" model { file = "/net/cci-nas-00/data/ceres_data/9mtc_48605/02_2026/9mtc_48605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtc_48605/02_2026/9mtc_48605.cif" } resolution = 2.63 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 164 5.16 5 C 19940 2.51 5 N 5420 2.21 5 O 5428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30964 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 7710 Classifications: {'peptide': 969} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 927} Chain breaks: 8 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, C, D Time building chain proxies: 7.59, per 1000 atoms: 0.25 Number of scatterers: 30964 At special positions: 0 Unit cell: (157.388, 157.388, 156.613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 164 16.00 P 12 15.00 O 5428 8.00 N 5420 7.00 C 19940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7184 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 12 sheets defined 68.8% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.614A pdb=" N ILE B 14 " --> pdb=" O TRP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.843A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.677A pdb=" N THR B 199 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.594A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.901A pdb=" N LYS B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.552A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 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 465 Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.725A pdb=" N ARG B 601 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.614A pdb=" N GLY B 650 " --> pdb=" O PRO B 647 " (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 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 769 through 778 removed outlier: 3.539A pdb=" N ALA B 778 " --> pdb=" O HIS B 774 " (cutoff:3.500A) 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 904 removed outlier: 3.579A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 removed outlier: 4.355A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 924 removed outlier: 3.700A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 974 removed outlier: 5.047A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix removed outlier: 3.612A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 removed outlier: 3.575A pdb=" N MET B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.539A pdb=" N ILE B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1090 removed outlier: 4.102A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 Processing helix chain 'B' and resid 1143 through 1168 removed outlier: 3.829A pdb=" N TYR B1168 " --> pdb=" O HIS B1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.612A pdb=" N ILE A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.843A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.677A pdb=" N THR A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.594A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.901A pdb=" N LYS A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.552A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 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 465 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.725A pdb=" N ARG A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 644 Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.614A pdb=" N GLY A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) 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 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 769 through 778 removed outlier: 3.539A pdb=" N ALA A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) 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 904 removed outlier: 3.580A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 removed outlier: 4.355A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.700A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 974 removed outlier: 5.046A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.613A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.577A pdb=" N MET A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.539A pdb=" N ILE A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1090 removed outlier: 4.102A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 Processing helix chain 'A' and resid 1143 through 1168 removed outlier: 3.829A pdb=" N TYR A1168 " --> pdb=" O HIS A1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.614A pdb=" N ILE C 14 " --> pdb=" O TRP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.843A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.677A 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 281 through 294 Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.594A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.900A pdb=" N LYS C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.552A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 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 465 Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.725A pdb=" N ARG C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 644 Processing helix chain 'C' and resid 646 through 650 removed outlier: 3.614A pdb=" N GLY C 650 " --> pdb=" O PRO C 647 " (cutoff:3.500A) 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 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 769 through 778 removed outlier: 3.538A pdb=" N ALA C 778 " --> pdb=" O HIS C 774 " (cutoff:3.500A) 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 904 removed outlier: 3.579A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 911 removed outlier: 4.355A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 924 removed outlier: 3.700A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 974 removed outlier: 5.045A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix removed outlier: 3.612A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 removed outlier: 3.577A pdb=" N MET C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.540A pdb=" N ILE C1033 " --> pdb=" O LEU C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1090 removed outlier: 4.102A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 Processing helix chain 'C' and resid 1143 through 1168 removed outlier: 3.829A pdb=" N TYR C1168 " --> pdb=" O HIS C1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.614A pdb=" N ILE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.843A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.677A pdb=" N THR D 199 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.595A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.901A pdb=" N LYS D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.552A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 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 465 Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.725A pdb=" N ARG D 601 " --> pdb=" O ARG D 597 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 644 Processing helix chain 'D' and resid 646 through 650 removed outlier: 3.622A pdb=" N GLY D 650 " --> pdb=" O PRO D 647 " (cutoff:3.500A) 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 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 769 through 778 removed outlier: 3.540A pdb=" N ALA D 778 " --> pdb=" O HIS D 774 " (cutoff:3.500A) 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 904 removed outlier: 3.580A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 911 removed outlier: 4.355A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 924 removed outlier: 3.715A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 974 removed outlier: 5.041A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix removed outlier: 3.610A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 984 removed outlier: 3.577A pdb=" N MET D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.538A pdb=" N ILE D1033 " --> pdb=" O LEU D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1072 removed outlier: 5.408A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1090 removed outlier: 4.102A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 Processing helix chain 'D' and resid 1143 through 1168 removed outlier: 3.830A pdb=" N TYR D1168 " --> pdb=" O HIS D1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 211 removed outlier: 4.558A pdb=" N PHE B 207 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 119 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 278 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU B 122 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.107A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 211 removed outlier: 4.558A pdb=" N PHE A 207 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE A 278 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU A 122 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.107A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 16 through 20 Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 211 removed outlier: 4.558A pdb=" N PHE C 207 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE C 278 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU C 122 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.107A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 20 Processing sheet with id=AB2, first strand: chain 'D' and resid 206 through 211 removed outlier: 4.557A pdb=" N PHE D 207 " --> pdb=" O TYR D 75 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 119 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE D 278 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU D 122 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.107A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1868 hydrogen bonds defined for protein. 5496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6330 1.33 - 1.45: 7516 1.45 - 1.57: 17578 1.57 - 1.69: 20 1.69 - 1.81: 252 Bond restraints: 31696 Sorted by residual: bond pdb=" O2A ATP A2001 " pdb=" PA ATP A2001 " ideal model delta sigma weight residual 1.529 1.481 0.048 2.20e-02 2.07e+03 4.70e+00 bond pdb=" O2A ATP C2001 " pdb=" PA ATP C2001 " ideal model delta sigma weight residual 1.529 1.481 0.048 2.20e-02 2.07e+03 4.70e+00 bond pdb=" O2A ATP B2001 " pdb=" PA ATP B2001 " ideal model delta sigma weight residual 1.529 1.481 0.048 2.20e-02 2.07e+03 4.70e+00 bond pdb=" O2B ATP B2001 " pdb=" PB ATP B2001 " ideal model delta sigma weight residual 1.529 1.482 0.047 2.20e-02 2.07e+03 4.64e+00 bond pdb=" O2B ATP A2001 " pdb=" PB ATP A2001 " ideal model delta sigma weight residual 1.529 1.482 0.047 2.20e-02 2.07e+03 4.64e+00 ... (remaining 31691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 42136 1.49 - 2.99: 687 2.99 - 4.48: 118 4.48 - 5.98: 31 5.98 - 7.47: 12 Bond angle restraints: 42984 Sorted by residual: angle pdb=" PA ATP B2001 " pdb=" O3A ATP B2001 " pdb=" PB ATP B2001 " ideal model delta sigma weight residual 136.83 131.64 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" PA ATP A2001 " pdb=" O3A ATP A2001 " pdb=" PB ATP A2001 " ideal model delta sigma weight residual 136.83 131.64 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" PA ATP C2001 " pdb=" O3A ATP C2001 " pdb=" PB ATP C2001 " ideal model delta sigma weight residual 136.83 131.65 5.18 1.00e+00 1.00e+00 2.69e+01 angle pdb=" PA ATP D2001 " pdb=" O3A ATP D2001 " pdb=" PB ATP D2001 " ideal model delta sigma weight residual 136.83 131.70 5.13 1.00e+00 1.00e+00 2.64e+01 angle pdb=" O1G ATP C2001 " pdb=" PG ATP C2001 " pdb=" O3B ATP C2001 " ideal model delta sigma weight residual 110.47 105.23 5.24 1.64e+00 3.70e-01 1.02e+01 ... (remaining 42979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 17593 17.87 - 35.74: 877 35.74 - 53.60: 226 53.60 - 71.47: 56 71.47 - 89.34: 12 Dihedral angle restraints: 18764 sinusoidal: 7640 harmonic: 11124 Sorted by residual: dihedral pdb=" CA ASN D 584 " pdb=" C ASN D 584 " pdb=" N ALA D 585 " pdb=" CA ALA D 585 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN B 584 " pdb=" C ASN B 584 " pdb=" N ALA B 585 " pdb=" CA ALA B 585 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN C 584 " pdb=" C ASN C 584 " pdb=" N ALA C 585 " pdb=" CA ALA C 585 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 18761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2869 0.027 - 0.055: 1351 0.055 - 0.082: 381 0.082 - 0.110: 183 0.110 - 0.137: 12 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CA ILE C 278 " pdb=" N ILE C 278 " pdb=" C ILE C 278 " pdb=" CB ILE C 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 278 " pdb=" N ILE A 278 " pdb=" C ILE A 278 " pdb=" CB ILE A 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE B 278 " pdb=" N ILE B 278 " pdb=" C ILE B 278 " pdb=" CB ILE B 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 4793 not shown) Planarity restraints: 5412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 20 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C CYS A 20 " 0.067 2.00e-02 2.50e+03 pdb=" O CYS A 20 " -0.026 2.00e-02 2.50e+03 pdb=" N THR A 21 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 20 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C CYS B 20 " 0.067 2.00e-02 2.50e+03 pdb=" O CYS B 20 " -0.026 2.00e-02 2.50e+03 pdb=" N THR B 21 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 20 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C CYS C 20 " 0.067 2.00e-02 2.50e+03 pdb=" O CYS C 20 " -0.026 2.00e-02 2.50e+03 pdb=" N THR C 21 " -0.023 2.00e-02 2.50e+03 ... (remaining 5409 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4415 2.76 - 3.29: 29888 3.29 - 3.83: 53405 3.83 - 4.36: 63373 4.36 - 4.90: 108361 Nonbonded interactions: 259442 Sorted by model distance: nonbonded pdb=" O ASP D 317 " pdb=" O THR D 318 " model vdw 2.221 3.040 nonbonded pdb=" O ASP A 317 " pdb=" O THR A 318 " model vdw 2.221 3.040 nonbonded pdb=" O ASP B 317 " pdb=" O THR B 318 " model vdw 2.221 3.040 nonbonded pdb=" O ASP C 317 " pdb=" O THR C 318 " model vdw 2.221 3.040 nonbonded pdb=" O ASP A 317 " pdb=" OG1 THR A 318 " model vdw 2.385 3.040 ... (remaining 259437 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: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.630 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.470 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 0.048 31696 Z= 0.144 Angle : 0.513 7.474 42984 Z= 0.279 Chirality : 0.036 0.137 4796 Planarity : 0.004 0.039 5412 Dihedral : 12.051 89.341 11580 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.83 % Allowed : 4.27 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.14), residues: 3804 helix: 1.72 (0.11), residues: 2460 sheet: -0.17 (0.35), residues: 268 loop : -0.37 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 637 TYR 0.015 0.001 TYR B 227 PHE 0.012 0.001 PHE D 627 TRP 0.013 0.001 TRP A1124 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00315 (31696) covalent geometry : angle 0.51264 (42984) hydrogen bonds : bond 0.11344 ( 1868) hydrogen bonds : angle 5.90120 ( 5496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 424 time to evaluate : 1.174 Fit side-chains REVERT: B 132 THR cc_start: 0.8107 (m) cc_final: 0.7883 (t) REVERT: B 140 ARG cc_start: 0.8512 (mmt180) cc_final: 0.8280 (mmt-90) REVERT: B 202 ASN cc_start: 0.8061 (t0) cc_final: 0.7798 (t0) REVERT: B 284 MET cc_start: 0.7890 (tpp) cc_final: 0.7502 (mmp) REVERT: B 293 GLN cc_start: 0.7861 (tt0) cc_final: 0.7399 (mm110) REVERT: B 414 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: B 475 ASN cc_start: 0.7330 (t0) cc_final: 0.7120 (t0) REVERT: B 505 HIS cc_start: 0.7307 (m90) cc_final: 0.6621 (t70) REVERT: B 635 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7715 (mp0) REVERT: B 662 ASP cc_start: 0.8014 (m-30) cc_final: 0.7653 (t70) REVERT: B 684 MET cc_start: 0.8866 (mtm) cc_final: 0.8617 (mtt) REVERT: B 689 PRO cc_start: 0.8323 (Cg_exo) cc_final: 0.8073 (Cg_endo) REVERT: B 695 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7797 (tp) REVERT: B 769 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6992 (mm) REVERT: B 1053 ASN cc_start: 0.8591 (m110) cc_final: 0.8178 (m-40) REVERT: A 132 THR cc_start: 0.8031 (m) cc_final: 0.7797 (t) REVERT: A 140 ARG cc_start: 0.8455 (mmt180) cc_final: 0.8202 (mmt-90) REVERT: A 202 ASN cc_start: 0.7988 (t0) cc_final: 0.7713 (t0) REVERT: A 284 MET cc_start: 0.7818 (tpp) cc_final: 0.7428 (mmp) REVERT: A 293 GLN cc_start: 0.7808 (tt0) cc_final: 0.7305 (mm110) REVERT: A 414 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: A 475 ASN cc_start: 0.7234 (t0) cc_final: 0.7014 (t0) REVERT: A 505 HIS cc_start: 0.7198 (m90) cc_final: 0.6504 (t70) REVERT: A 635 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7658 (mp0) REVERT: A 662 ASP cc_start: 0.8079 (m-30) cc_final: 0.7626 (t70) REVERT: A 684 MET cc_start: 0.8846 (mtm) cc_final: 0.8597 (mtt) REVERT: A 689 PRO cc_start: 0.8268 (Cg_exo) cc_final: 0.8009 (Cg_endo) REVERT: A 695 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7749 (tp) REVERT: A 769 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6961 (mm) REVERT: A 1053 ASN cc_start: 0.8552 (m110) cc_final: 0.8135 (m-40) REVERT: C 132 THR cc_start: 0.8032 (m) cc_final: 0.7800 (t) REVERT: C 140 ARG cc_start: 0.8435 (mmt180) cc_final: 0.8176 (mmt-90) REVERT: C 202 ASN cc_start: 0.7984 (t0) cc_final: 0.7703 (t0) REVERT: C 284 MET cc_start: 0.7811 (tpp) cc_final: 0.7420 (mmp) REVERT: C 293 GLN cc_start: 0.7801 (tt0) cc_final: 0.7297 (mm110) REVERT: C 414 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: C 475 ASN cc_start: 0.7226 (t0) cc_final: 0.7010 (t0) REVERT: C 505 HIS cc_start: 0.7193 (m90) cc_final: 0.6499 (t70) REVERT: C 635 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7609 (mp0) REVERT: C 662 ASP cc_start: 0.8008 (m-30) cc_final: 0.7596 (t70) REVERT: C 684 MET cc_start: 0.8844 (mtm) cc_final: 0.8595 (mtt) REVERT: C 689 PRO cc_start: 0.8249 (Cg_exo) cc_final: 0.7990 (Cg_endo) REVERT: C 695 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7744 (tp) REVERT: C 769 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6961 (mm) REVERT: C 1053 ASN cc_start: 0.8504 (m110) cc_final: 0.8082 (m-40) REVERT: D 132 THR cc_start: 0.8031 (m) cc_final: 0.7803 (t) REVERT: D 140 ARG cc_start: 0.8443 (mmt180) cc_final: 0.8180 (mmt-90) REVERT: D 202 ASN cc_start: 0.7976 (t0) cc_final: 0.7696 (t0) REVERT: D 284 MET cc_start: 0.7806 (tpp) cc_final: 0.7414 (mmp) REVERT: D 293 GLN cc_start: 0.7822 (tt0) cc_final: 0.7307 (mm110) REVERT: D 414 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7009 (m-80) REVERT: D 475 ASN cc_start: 0.7225 (t0) cc_final: 0.7010 (t0) REVERT: D 505 HIS cc_start: 0.7197 (m90) cc_final: 0.6502 (t70) REVERT: D 635 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7608 (mp0) REVERT: D 662 ASP cc_start: 0.8033 (m-30) cc_final: 0.7587 (t70) REVERT: D 684 MET cc_start: 0.8848 (mtm) cc_final: 0.8595 (mtt) REVERT: D 689 PRO cc_start: 0.8244 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: D 695 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7743 (tp) REVERT: D 769 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6954 (mm) REVERT: D 1053 ASN cc_start: 0.8551 (m110) cc_final: 0.8129 (m-40) outliers start: 60 outliers final: 24 residues processed: 464 average time/residue: 0.7450 time to fit residues: 402.6245 Evaluate side-chains 364 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 328 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 985 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 295 GLN A 66 HIS A 295 GLN C 66 HIS C 295 GLN D 66 HIS D 295 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110446 restraints weight = 33915.148| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.98 r_work: 0.3085 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 31696 Z= 0.264 Angle : 0.638 8.151 42984 Z= 0.322 Chirality : 0.044 0.202 4796 Planarity : 0.005 0.058 5412 Dihedral : 7.683 88.434 4424 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.96 % Allowed : 7.97 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.29 (0.14), residues: 3804 helix: 1.53 (0.10), residues: 2468 sheet: -0.08 (0.33), residues: 308 loop : -0.36 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 113 TYR 0.024 0.002 TYR C 227 PHE 0.018 0.002 PHE A1069 TRP 0.016 0.002 TRP D1058 HIS 0.008 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00645 (31696) covalent geometry : angle 0.63756 (42984) hydrogen bonds : bond 0.05530 ( 1868) hydrogen bonds : angle 4.77585 ( 5496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 336 time to evaluate : 1.221 Fit side-chains REVERT: B 140 ARG cc_start: 0.8472 (mmt180) cc_final: 0.8153 (mmt-90) REVERT: B 202 ASN cc_start: 0.7995 (t0) cc_final: 0.7739 (t0) REVERT: B 204 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7291 (mtpp) REVERT: B 210 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7322 (mtm110) REVERT: B 284 MET cc_start: 0.7907 (tpp) cc_final: 0.7548 (mmp) REVERT: B 289 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: B 293 GLN cc_start: 0.7778 (tt0) cc_final: 0.7189 (mm110) REVERT: B 348 GLN cc_start: 0.7297 (tp40) cc_final: 0.7081 (tp40) REVERT: B 371 GLU cc_start: 0.7800 (pm20) cc_final: 0.7598 (pm20) REVERT: B 505 HIS cc_start: 0.7272 (m90) cc_final: 0.6615 (t70) REVERT: B 635 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7563 (mp0) REVERT: B 662 ASP cc_start: 0.8011 (m-30) cc_final: 0.7563 (t70) REVERT: B 695 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 769 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6868 (mm) REVERT: B 915 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6581 (mm-40) REVERT: B 1053 ASN cc_start: 0.8560 (m110) cc_final: 0.8126 (m-40) REVERT: B 1116 GLU cc_start: 0.7637 (mp0) cc_final: 0.7204 (tm-30) REVERT: A 140 ARG cc_start: 0.8469 (mmt180) cc_final: 0.8146 (mmt-90) REVERT: A 202 ASN cc_start: 0.7999 (t0) cc_final: 0.7746 (t0) REVERT: A 204 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7274 (mtpp) REVERT: A 210 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7320 (mtm110) REVERT: A 284 MET cc_start: 0.7911 (tpp) cc_final: 0.7549 (mmp) REVERT: A 289 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: A 293 GLN cc_start: 0.7756 (tt0) cc_final: 0.7174 (mm110) REVERT: A 348 GLN cc_start: 0.7311 (tp40) cc_final: 0.7092 (tp40) REVERT: A 371 GLU cc_start: 0.7802 (pm20) cc_final: 0.7597 (pm20) REVERT: A 505 HIS cc_start: 0.7278 (m90) cc_final: 0.6624 (t70) REVERT: A 635 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7564 (mp0) REVERT: A 662 ASP cc_start: 0.8002 (m-30) cc_final: 0.7562 (t70) REVERT: A 695 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 769 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6870 (mm) REVERT: A 915 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6579 (mm-40) REVERT: A 1053 ASN cc_start: 0.8559 (m110) cc_final: 0.8124 (m-40) REVERT: A 1116 GLU cc_start: 0.7651 (mp0) cc_final: 0.7221 (tm-30) REVERT: C 140 ARG cc_start: 0.8462 (mmt180) cc_final: 0.8141 (mmt-90) REVERT: C 202 ASN cc_start: 0.7998 (t0) cc_final: 0.7744 (t0) REVERT: C 204 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7287 (mtpp) REVERT: C 210 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7289 (mtm110) REVERT: C 284 MET cc_start: 0.7906 (tpp) cc_final: 0.7542 (mmp) REVERT: C 289 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: C 293 GLN cc_start: 0.7760 (tt0) cc_final: 0.7174 (mm110) REVERT: C 348 GLN cc_start: 0.7311 (tp40) cc_final: 0.7095 (tp40) REVERT: C 371 GLU cc_start: 0.7818 (pm20) cc_final: 0.7616 (pm20) REVERT: C 505 HIS cc_start: 0.7256 (m90) cc_final: 0.6604 (t70) REVERT: C 635 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7554 (mp0) REVERT: C 662 ASP cc_start: 0.8023 (m-30) cc_final: 0.7561 (t70) REVERT: C 695 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8098 (tt) REVERT: C 769 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6877 (mm) REVERT: C 915 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6580 (mm-40) REVERT: C 1053 ASN cc_start: 0.8548 (m110) cc_final: 0.8108 (m-40) REVERT: C 1116 GLU cc_start: 0.7660 (mp0) cc_final: 0.7218 (tm-30) REVERT: D 140 ARG cc_start: 0.8461 (mmt180) cc_final: 0.8140 (mmt-90) REVERT: D 202 ASN cc_start: 0.7997 (t0) cc_final: 0.7741 (t0) REVERT: D 204 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7284 (mtpp) REVERT: D 210 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7310 (mtm110) REVERT: D 284 MET cc_start: 0.7915 (tpp) cc_final: 0.7553 (mmp) REVERT: D 289 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: D 293 GLN cc_start: 0.7761 (tt0) cc_final: 0.7179 (mm110) REVERT: D 348 GLN cc_start: 0.7299 (tp40) cc_final: 0.7079 (tp40) REVERT: D 371 GLU cc_start: 0.7807 (pm20) cc_final: 0.7602 (pm20) REVERT: D 505 HIS cc_start: 0.7269 (m90) cc_final: 0.6612 (t70) REVERT: D 635 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7577 (mp0) REVERT: D 662 ASP cc_start: 0.7997 (m-30) cc_final: 0.7552 (t70) REVERT: D 695 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8092 (tt) REVERT: D 769 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6881 (mm) REVERT: D 915 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6569 (mm-40) REVERT: D 1053 ASN cc_start: 0.8555 (m110) cc_final: 0.8119 (m-40) REVERT: D 1116 GLU cc_start: 0.7655 (mp0) cc_final: 0.7188 (tm-30) outliers start: 97 outliers final: 49 residues processed: 397 average time/residue: 0.6746 time to fit residues: 315.9802 Evaluate side-chains 386 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 313 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 993 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 281 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 351 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 295 GLN A 66 HIS A 295 GLN C 66 HIS C 295 GLN D 66 HIS D 295 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113475 restraints weight = 33964.357| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.99 r_work: 0.3138 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31696 Z= 0.125 Angle : 0.494 8.437 42984 Z= 0.250 Chirality : 0.036 0.166 4796 Planarity : 0.004 0.036 5412 Dihedral : 7.186 88.733 4416 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.96 % Allowed : 9.07 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.14), residues: 3804 helix: 1.94 (0.10), residues: 2464 sheet: 0.13 (0.36), residues: 268 loop : -0.38 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 113 TYR 0.012 0.001 TYR C 227 PHE 0.011 0.001 PHE D1069 TRP 0.012 0.001 TRP A1124 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00280 (31696) covalent geometry : angle 0.49441 (42984) hydrogen bonds : bond 0.04119 ( 1868) hydrogen bonds : angle 4.42671 ( 5496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 340 time to evaluate : 1.224 Fit side-chains REVERT: B 132 THR cc_start: 0.7961 (m) cc_final: 0.7716 (t) REVERT: B 140 ARG cc_start: 0.8344 (mmt180) cc_final: 0.8031 (mmt-90) REVERT: B 202 ASN cc_start: 0.7841 (t0) cc_final: 0.7574 (t0) REVERT: B 204 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7302 (mtpp) REVERT: B 210 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7170 (mtm110) REVERT: B 284 MET cc_start: 0.7802 (tpp) cc_final: 0.7434 (mmp) REVERT: B 293 GLN cc_start: 0.7805 (tt0) cc_final: 0.7239 (mm110) REVERT: B 475 ASN cc_start: 0.7303 (t0) cc_final: 0.7070 (t0) REVERT: B 505 HIS cc_start: 0.7234 (m90) cc_final: 0.6607 (t70) REVERT: B 635 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7530 (mp0) REVERT: B 659 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8850 (ttp) REVERT: B 662 ASP cc_start: 0.8050 (m-30) cc_final: 0.7599 (t0) REVERT: B 695 LEU cc_start: 0.8261 (mt) cc_final: 0.7706 (tp) REVERT: B 769 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6856 (mm) REVERT: B 915 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6526 (mm-40) REVERT: B 1053 ASN cc_start: 0.8479 (m110) cc_final: 0.8046 (m-40) REVERT: A 132 THR cc_start: 0.7961 (m) cc_final: 0.7709 (t) REVERT: A 140 ARG cc_start: 0.8348 (mmt180) cc_final: 0.8035 (mmt-90) REVERT: A 202 ASN cc_start: 0.7848 (t0) cc_final: 0.7585 (t0) REVERT: A 204 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7301 (mtpp) REVERT: A 210 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7174 (mtm110) REVERT: A 284 MET cc_start: 0.7802 (tpp) cc_final: 0.7446 (mmp) REVERT: A 293 GLN cc_start: 0.7820 (tt0) cc_final: 0.7241 (mm110) REVERT: A 371 GLU cc_start: 0.7749 (pm20) cc_final: 0.7547 (pm20) REVERT: A 475 ASN cc_start: 0.7306 (t0) cc_final: 0.7075 (t0) REVERT: A 505 HIS cc_start: 0.7248 (m90) cc_final: 0.6626 (t70) REVERT: A 635 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7535 (mp0) REVERT: A 659 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8851 (ttp) REVERT: A 662 ASP cc_start: 0.8076 (m-30) cc_final: 0.7621 (t0) REVERT: A 695 LEU cc_start: 0.8257 (mt) cc_final: 0.7698 (tp) REVERT: A 769 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6851 (mm) REVERT: A 915 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6523 (mm-40) REVERT: A 1053 ASN cc_start: 0.8469 (m110) cc_final: 0.8034 (m-40) REVERT: C 132 THR cc_start: 0.7936 (m) cc_final: 0.7701 (t) REVERT: C 140 ARG cc_start: 0.8338 (mmt180) cc_final: 0.8029 (mmt-90) REVERT: C 202 ASN cc_start: 0.7849 (t0) cc_final: 0.7584 (t0) REVERT: C 204 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7313 (mtpp) REVERT: C 210 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7151 (mtm110) REVERT: C 284 MET cc_start: 0.7789 (tpp) cc_final: 0.7427 (mmp) REVERT: C 293 GLN cc_start: 0.7819 (tt0) cc_final: 0.7240 (mm110) REVERT: C 475 ASN cc_start: 0.7321 (t0) cc_final: 0.7091 (t0) REVERT: C 505 HIS cc_start: 0.7218 (m90) cc_final: 0.6593 (t70) REVERT: C 635 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7526 (mp0) REVERT: C 659 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8848 (ttp) REVERT: C 662 ASP cc_start: 0.8076 (m-30) cc_final: 0.7618 (t0) REVERT: C 695 LEU cc_start: 0.8260 (mt) cc_final: 0.7710 (tp) REVERT: C 769 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6868 (mm) REVERT: C 915 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6530 (mm-40) REVERT: C 1053 ASN cc_start: 0.8462 (m110) cc_final: 0.8022 (m-40) REVERT: D 132 THR cc_start: 0.7975 (m) cc_final: 0.7725 (t) REVERT: D 140 ARG cc_start: 0.8345 (mmt180) cc_final: 0.8033 (mmt-90) REVERT: D 202 ASN cc_start: 0.7834 (t0) cc_final: 0.7567 (t0) REVERT: D 204 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7306 (mtpp) REVERT: D 210 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7177 (mtm110) REVERT: D 284 MET cc_start: 0.7813 (tpp) cc_final: 0.7445 (mmp) REVERT: D 293 GLN cc_start: 0.7816 (tt0) cc_final: 0.7244 (mm110) REVERT: D 371 GLU cc_start: 0.7744 (pm20) cc_final: 0.7538 (pm20) REVERT: D 475 ASN cc_start: 0.7307 (t0) cc_final: 0.7078 (t0) REVERT: D 505 HIS cc_start: 0.7225 (m90) cc_final: 0.6587 (t70) REVERT: D 635 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7557 (mp0) REVERT: D 659 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8856 (ttp) REVERT: D 662 ASP cc_start: 0.8044 (m-30) cc_final: 0.7599 (t0) REVERT: D 695 LEU cc_start: 0.8252 (mt) cc_final: 0.7704 (tp) REVERT: D 769 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6868 (mm) REVERT: D 915 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6516 (mm-40) REVERT: D 1053 ASN cc_start: 0.8472 (m110) cc_final: 0.8032 (m-40) outliers start: 97 outliers final: 43 residues processed: 402 average time/residue: 0.6513 time to fit residues: 310.6103 Evaluate side-chains 373 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 310 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 305 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 347 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 356 optimal weight: 4.9990 chunk 271 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 295 GLN B 479 GLN B1014 GLN A 66 HIS A 295 GLN A 479 GLN A1014 GLN C 66 HIS C 295 GLN C 479 GLN C1014 GLN D 66 HIS D 295 GLN D 479 GLN D1014 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135576 restraints weight = 35012.358| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.42 r_work: 0.3397 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31696 Z= 0.102 Angle : 0.454 7.818 42984 Z= 0.233 Chirality : 0.035 0.151 4796 Planarity : 0.004 0.084 5412 Dihedral : 6.609 89.927 4400 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.08 % Allowed : 8.97 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.14), residues: 3804 helix: 2.17 (0.10), residues: 2472 sheet: 0.08 (0.35), residues: 284 loop : -0.29 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.010 0.001 TYR C 227 PHE 0.010 0.001 PHE C 423 TRP 0.013 0.001 TRP A1124 HIS 0.003 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00221 (31696) covalent geometry : angle 0.45422 (42984) hydrogen bonds : bond 0.03633 ( 1868) hydrogen bonds : angle 4.22411 ( 5496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 329 time to evaluate : 1.286 Fit side-chains REVERT: B 132 THR cc_start: 0.7992 (m) cc_final: 0.7786 (t) REVERT: B 140 ARG cc_start: 0.8248 (mmt180) cc_final: 0.7949 (mmt-90) REVERT: B 202 ASN cc_start: 0.8012 (t0) cc_final: 0.7757 (t0) REVERT: B 204 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7356 (mtpp) REVERT: B 210 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7105 (mtm110) REVERT: B 284 MET cc_start: 0.7813 (tpp) cc_final: 0.7460 (mmp) REVERT: B 289 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: B 293 GLN cc_start: 0.7843 (tt0) cc_final: 0.7380 (mm110) REVERT: B 475 ASN cc_start: 0.7362 (t0) cc_final: 0.7051 (t0) REVERT: B 505 HIS cc_start: 0.7285 (m90) cc_final: 0.6771 (t70) REVERT: B 635 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7519 (mp0) REVERT: B 662 ASP cc_start: 0.8034 (m-30) cc_final: 0.7592 (t0) REVERT: B 695 LEU cc_start: 0.8303 (mt) cc_final: 0.7737 (tp) REVERT: B 769 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6929 (mm) REVERT: B 915 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6571 (mm-40) REVERT: B 1053 ASN cc_start: 0.8372 (m110) cc_final: 0.7945 (m-40) REVERT: B 1116 GLU cc_start: 0.7479 (mp0) cc_final: 0.7139 (tm-30) REVERT: A 140 ARG cc_start: 0.8252 (mmt180) cc_final: 0.7954 (mmt-90) REVERT: A 202 ASN cc_start: 0.8022 (t0) cc_final: 0.7771 (t0) REVERT: A 204 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7349 (mtpp) REVERT: A 210 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7117 (mtm110) REVERT: A 284 MET cc_start: 0.7785 (tpp) cc_final: 0.7431 (mmp) REVERT: A 289 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: A 293 GLN cc_start: 0.7850 (tt0) cc_final: 0.7381 (mm110) REVERT: A 475 ASN cc_start: 0.7376 (t0) cc_final: 0.7069 (t0) REVERT: A 505 HIS cc_start: 0.7264 (m90) cc_final: 0.6745 (t70) REVERT: A 635 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 662 ASP cc_start: 0.8021 (m-30) cc_final: 0.7595 (t0) REVERT: A 695 LEU cc_start: 0.8299 (mt) cc_final: 0.7725 (tp) REVERT: A 769 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6929 (mm) REVERT: A 915 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6581 (mm-40) REVERT: A 1053 ASN cc_start: 0.8377 (m110) cc_final: 0.7951 (m-40) REVERT: A 1116 GLU cc_start: 0.7463 (mp0) cc_final: 0.7154 (tm-30) REVERT: C 132 THR cc_start: 0.7980 (m) cc_final: 0.7778 (t) REVERT: C 140 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7928 (mmt-90) REVERT: C 202 ASN cc_start: 0.8030 (t0) cc_final: 0.7779 (t0) REVERT: C 204 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7369 (mtpp) REVERT: C 210 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7098 (mtm110) REVERT: C 284 MET cc_start: 0.7800 (tpp) cc_final: 0.7445 (mmp) REVERT: C 289 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: C 293 GLN cc_start: 0.7852 (tt0) cc_final: 0.7378 (mm110) REVERT: C 475 ASN cc_start: 0.7351 (t0) cc_final: 0.7040 (t0) REVERT: C 505 HIS cc_start: 0.7269 (m90) cc_final: 0.6747 (t70) REVERT: C 635 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7534 (mp0) REVERT: C 662 ASP cc_start: 0.8059 (m-30) cc_final: 0.7606 (t0) REVERT: C 695 LEU cc_start: 0.8295 (mt) cc_final: 0.7725 (tp) REVERT: C 769 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6933 (mm) REVERT: C 915 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6548 (mm-40) REVERT: C 1053 ASN cc_start: 0.8381 (m110) cc_final: 0.7953 (m-40) REVERT: C 1116 GLU cc_start: 0.7463 (mp0) cc_final: 0.7131 (tm-30) REVERT: D 132 THR cc_start: 0.7983 (m) cc_final: 0.7778 (t) REVERT: D 140 ARG cc_start: 0.8249 (mmt180) cc_final: 0.7950 (mmt-90) REVERT: D 202 ASN cc_start: 0.8016 (t0) cc_final: 0.7759 (t0) REVERT: D 204 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7343 (mtpp) REVERT: D 210 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7077 (mtm110) REVERT: D 284 MET cc_start: 0.7802 (tpp) cc_final: 0.7454 (mmp) REVERT: D 289 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: D 293 GLN cc_start: 0.7850 (tt0) cc_final: 0.7372 (mm110) REVERT: D 371 GLU cc_start: 0.7779 (pm20) cc_final: 0.7570 (pm20) REVERT: D 475 ASN cc_start: 0.7370 (t0) cc_final: 0.7046 (t0) REVERT: D 505 HIS cc_start: 0.7269 (m90) cc_final: 0.6751 (t70) REVERT: D 635 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7533 (mp0) REVERT: D 662 ASP cc_start: 0.8039 (m-30) cc_final: 0.7615 (t0) REVERT: D 695 LEU cc_start: 0.8300 (mt) cc_final: 0.7731 (tp) REVERT: D 769 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6934 (mm) REVERT: D 915 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6552 (mm-40) REVERT: D 1053 ASN cc_start: 0.8372 (m110) cc_final: 0.7939 (m-40) REVERT: D 1116 GLU cc_start: 0.7509 (mp0) cc_final: 0.7158 (tm-30) outliers start: 101 outliers final: 41 residues processed: 397 average time/residue: 0.7269 time to fit residues: 339.3365 Evaluate side-chains 357 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1109 PHE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain D residue 1113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 361 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 295 GLN A 66 HIS A 295 GLN C 66 HIS C 295 GLN D 66 HIS D 295 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.168793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131986 restraints weight = 35177.201| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.50 r_work: 0.3338 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 31696 Z= 0.236 Angle : 0.594 7.980 42984 Z= 0.301 Chirality : 0.041 0.196 4796 Planarity : 0.005 0.081 5412 Dihedral : 6.716 87.441 4396 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.48 % Allowed : 9.16 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.57 (0.14), residues: 3804 helix: 1.77 (0.10), residues: 2472 sheet: -0.10 (0.33), residues: 324 loop : -0.31 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 113 TYR 0.020 0.002 TYR A 227 PHE 0.018 0.002 PHE D1069 TRP 0.015 0.002 TRP A1058 HIS 0.007 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00569 (31696) covalent geometry : angle 0.59398 (42984) hydrogen bonds : bond 0.05108 ( 1868) hydrogen bonds : angle 4.51117 ( 5496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 312 time to evaluate : 1.275 Fit side-chains REVERT: B 132 THR cc_start: 0.8043 (m) cc_final: 0.7815 (t) REVERT: B 140 ARG cc_start: 0.8432 (mmt180) cc_final: 0.8140 (mmt-90) REVERT: B 202 ASN cc_start: 0.8052 (t0) cc_final: 0.7833 (t0) REVERT: B 204 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7295 (mtpp) REVERT: B 210 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7245 (mtm110) REVERT: B 284 MET cc_start: 0.7914 (tpp) cc_final: 0.7575 (mmp) REVERT: B 289 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: B 293 GLN cc_start: 0.7860 (tt0) cc_final: 0.7473 (mm110) REVERT: B 475 ASN cc_start: 0.7473 (t0) cc_final: 0.7219 (t0) REVERT: B 505 HIS cc_start: 0.7438 (m90) cc_final: 0.6863 (t70) REVERT: B 635 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7521 (mp0) REVERT: B 662 ASP cc_start: 0.7991 (m-30) cc_final: 0.7560 (t70) REVERT: B 769 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6887 (mm) REVERT: B 915 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6614 (mm-40) REVERT: B 926 MET cc_start: 0.8996 (mmt) cc_final: 0.8259 (mmt) REVERT: B 1053 ASN cc_start: 0.8475 (m110) cc_final: 0.8056 (m-40) REVERT: A 140 ARG cc_start: 0.8427 (mmt180) cc_final: 0.8136 (mmt-90) REVERT: A 202 ASN cc_start: 0.8057 (t0) cc_final: 0.7842 (t0) REVERT: A 204 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7288 (mtpp) REVERT: A 210 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7262 (mtm110) REVERT: A 284 MET cc_start: 0.7900 (tpp) cc_final: 0.7559 (mmp) REVERT: A 289 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 293 GLN cc_start: 0.7866 (tt0) cc_final: 0.7468 (mm110) REVERT: A 371 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: A 475 ASN cc_start: 0.7490 (t0) cc_final: 0.7238 (t0) REVERT: A 505 HIS cc_start: 0.7409 (m90) cc_final: 0.6839 (t70) REVERT: A 635 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7538 (mp0) REVERT: A 662 ASP cc_start: 0.7966 (m-30) cc_final: 0.7558 (t70) REVERT: A 769 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6887 (mm) REVERT: A 915 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6640 (mm-40) REVERT: A 926 MET cc_start: 0.8985 (mmt) cc_final: 0.8237 (mmt) REVERT: A 1053 ASN cc_start: 0.8490 (m110) cc_final: 0.8074 (m-40) REVERT: C 132 THR cc_start: 0.8042 (m) cc_final: 0.7821 (t) REVERT: C 140 ARG cc_start: 0.8419 (mmt180) cc_final: 0.8115 (mmt-90) REVERT: C 202 ASN cc_start: 0.8059 (t0) cc_final: 0.7844 (t0) REVERT: C 204 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7305 (mtpp) REVERT: C 210 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7230 (mtm110) REVERT: C 284 MET cc_start: 0.7910 (tpp) cc_final: 0.7567 (mmp) REVERT: C 289 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: C 293 GLN cc_start: 0.7873 (tt0) cc_final: 0.7470 (mm110) REVERT: C 475 ASN cc_start: 0.7485 (t0) cc_final: 0.7231 (t0) REVERT: C 505 HIS cc_start: 0.7416 (m90) cc_final: 0.6842 (t70) REVERT: C 635 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7519 (mp0) REVERT: C 662 ASP cc_start: 0.7982 (m-30) cc_final: 0.7559 (t70) REVERT: C 769 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6888 (mm) REVERT: C 915 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6633 (mm-40) REVERT: C 926 MET cc_start: 0.8991 (mmt) cc_final: 0.8256 (mmt) REVERT: C 1053 ASN cc_start: 0.8482 (m110) cc_final: 0.8064 (m-40) REVERT: D 132 THR cc_start: 0.8024 (m) cc_final: 0.7790 (t) REVERT: D 140 ARG cc_start: 0.8425 (mmt180) cc_final: 0.8130 (mmt-90) REVERT: D 202 ASN cc_start: 0.8049 (t0) cc_final: 0.7829 (t0) REVERT: D 204 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7301 (mtpp) REVERT: D 210 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7234 (mtm110) REVERT: D 284 MET cc_start: 0.7904 (tpp) cc_final: 0.7566 (mmp) REVERT: D 289 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: D 293 GLN cc_start: 0.7856 (tt0) cc_final: 0.7474 (mm110) REVERT: D 371 GLU cc_start: 0.7883 (pm20) cc_final: 0.7652 (pm20) REVERT: D 475 ASN cc_start: 0.7473 (t0) cc_final: 0.7216 (t0) REVERT: D 505 HIS cc_start: 0.7418 (m90) cc_final: 0.6851 (t70) REVERT: D 635 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7520 (mp0) REVERT: D 662 ASP cc_start: 0.7992 (m-30) cc_final: 0.7559 (t70) REVERT: D 769 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6887 (mm) REVERT: D 915 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6611 (mm-40) REVERT: D 1053 ASN cc_start: 0.8474 (m110) cc_final: 0.8056 (m-40) outliers start: 114 outliers final: 60 residues processed: 386 average time/residue: 0.6642 time to fit residues: 306.5608 Evaluate side-chains 389 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 308 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 985 VAL Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 985 VAL Chi-restraints excluded: chain D residue 993 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 277 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 127 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 373 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B1014 GLN A 66 HIS A1014 GLN C 66 HIS C1014 GLN D 66 HIS D1014 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.171918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127025 restraints weight = 35393.667| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.68 r_work: 0.3392 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 31696 Z= 0.112 Angle : 0.479 8.664 42984 Z= 0.246 Chirality : 0.035 0.161 4796 Planarity : 0.004 0.070 5412 Dihedral : 6.517 89.099 4396 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.66 % Allowed : 10.01 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.92 (0.14), residues: 3804 helix: 2.09 (0.10), residues: 2468 sheet: 0.09 (0.36), residues: 284 loop : -0.30 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 113 TYR 0.012 0.001 TYR C 227 PHE 0.010 0.001 PHE D1069 TRP 0.012 0.001 TRP D1124 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00246 (31696) covalent geometry : angle 0.47938 (42984) hydrogen bonds : bond 0.03836 ( 1868) hydrogen bonds : angle 4.29640 ( 5496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 314 time to evaluate : 0.958 Fit side-chains REVERT: B 132 THR cc_start: 0.8028 (m) cc_final: 0.7816 (t) REVERT: B 140 ARG cc_start: 0.8350 (mmt180) cc_final: 0.8066 (mmt-90) REVERT: B 202 ASN cc_start: 0.8005 (t0) cc_final: 0.7767 (t0) REVERT: B 204 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7720 (mtpp) REVERT: B 210 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7216 (mtm110) REVERT: B 284 MET cc_start: 0.7889 (tpp) cc_final: 0.7552 (mmp) REVERT: B 289 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: B 293 GLN cc_start: 0.7606 (tt0) cc_final: 0.7063 (mm110) REVERT: B 475 ASN cc_start: 0.7388 (t0) cc_final: 0.7134 (t0) REVERT: B 505 HIS cc_start: 0.7326 (m90) cc_final: 0.6754 (t70) REVERT: B 635 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7539 (mp0) REVERT: B 662 ASP cc_start: 0.8104 (m-30) cc_final: 0.7675 (t0) REVERT: B 695 LEU cc_start: 0.8340 (mt) cc_final: 0.7775 (tp) REVERT: B 769 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6923 (mm) REVERT: B 915 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6665 (mm-40) REVERT: B 1053 ASN cc_start: 0.8447 (m110) cc_final: 0.8035 (m-40) REVERT: B 1116 GLU cc_start: 0.7572 (mp0) cc_final: 0.7250 (tm-30) REVERT: A 140 ARG cc_start: 0.8349 (mmt180) cc_final: 0.8066 (mmt-90) REVERT: A 202 ASN cc_start: 0.8000 (t0) cc_final: 0.7763 (t0) REVERT: A 204 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7718 (mtpp) REVERT: A 210 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7237 (mtm110) REVERT: A 284 MET cc_start: 0.7863 (tpp) cc_final: 0.7527 (mmp) REVERT: A 289 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: A 293 GLN cc_start: 0.7591 (tt0) cc_final: 0.7050 (mm110) REVERT: A 475 ASN cc_start: 0.7397 (t0) cc_final: 0.7146 (t0) REVERT: A 505 HIS cc_start: 0.7321 (m90) cc_final: 0.6747 (t70) REVERT: A 635 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7572 (mp0) REVERT: A 662 ASP cc_start: 0.8075 (m-30) cc_final: 0.7676 (t0) REVERT: A 695 LEU cc_start: 0.8336 (mt) cc_final: 0.7760 (tp) REVERT: A 769 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6929 (mm) REVERT: A 915 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6664 (mm-40) REVERT: A 1053 ASN cc_start: 0.8464 (m110) cc_final: 0.8053 (m-40) REVERT: A 1116 GLU cc_start: 0.7577 (mp0) cc_final: 0.7267 (tm-30) REVERT: C 132 THR cc_start: 0.8027 (m) cc_final: 0.7826 (t) REVERT: C 140 ARG cc_start: 0.8340 (mmt180) cc_final: 0.8050 (mmt-90) REVERT: C 202 ASN cc_start: 0.8024 (t0) cc_final: 0.7788 (t0) REVERT: C 204 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7729 (mtpp) REVERT: C 210 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7193 (mtm110) REVERT: C 284 MET cc_start: 0.7895 (tpp) cc_final: 0.7552 (mmp) REVERT: C 289 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: C 293 GLN cc_start: 0.7613 (tt0) cc_final: 0.7064 (mm110) REVERT: C 475 ASN cc_start: 0.7383 (t0) cc_final: 0.7125 (t0) REVERT: C 505 HIS cc_start: 0.7293 (m90) cc_final: 0.6704 (t70) REVERT: C 635 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7568 (mp0) REVERT: C 662 ASP cc_start: 0.8112 (m-30) cc_final: 0.7690 (t0) REVERT: C 695 LEU cc_start: 0.8334 (mt) cc_final: 0.7769 (tp) REVERT: C 769 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6923 (mm) REVERT: C 915 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6636 (mm-40) REVERT: C 1053 ASN cc_start: 0.8482 (m110) cc_final: 0.8066 (m-40) REVERT: C 1116 GLU cc_start: 0.7565 (mp0) cc_final: 0.7252 (tm-30) REVERT: D 132 THR cc_start: 0.8027 (m) cc_final: 0.7809 (t) REVERT: D 140 ARG cc_start: 0.8353 (mmt180) cc_final: 0.8060 (mmt-90) REVERT: D 202 ASN cc_start: 0.7988 (t0) cc_final: 0.7747 (t0) REVERT: D 204 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7708 (mtpp) REVERT: D 210 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7199 (mtm110) REVERT: D 284 MET cc_start: 0.7888 (tpp) cc_final: 0.7554 (mmp) REVERT: D 289 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: D 293 GLN cc_start: 0.7617 (tt0) cc_final: 0.7052 (mm110) REVERT: D 475 ASN cc_start: 0.7429 (t0) cc_final: 0.7181 (t0) REVERT: D 505 HIS cc_start: 0.7301 (m90) cc_final: 0.6725 (t70) REVERT: D 635 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7539 (mp0) REVERT: D 662 ASP cc_start: 0.8108 (m-30) cc_final: 0.7684 (t70) REVERT: D 695 LEU cc_start: 0.8324 (mt) cc_final: 0.7760 (tp) REVERT: D 769 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6914 (mm) REVERT: D 915 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6626 (mm-40) REVERT: D 1053 ASN cc_start: 0.8461 (m110) cc_final: 0.8050 (m-40) REVERT: D 1116 GLU cc_start: 0.7574 (mp0) cc_final: 0.7258 (tm-30) outliers start: 87 outliers final: 32 residues processed: 373 average time/residue: 0.6840 time to fit residues: 300.5066 Evaluate side-chains 349 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 135 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 354 optimal weight: 0.8980 chunk 337 optimal weight: 8.9990 chunk 368 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 168 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B1014 GLN A 66 HIS A1014 GLN C 66 HIS C1014 GLN D 66 HIS D1014 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.166039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119691 restraints weight = 34843.769| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.81 r_work: 0.3259 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31696 Z= 0.137 Angle : 0.497 7.577 42984 Z= 0.253 Chirality : 0.037 0.167 4796 Planarity : 0.004 0.065 5412 Dihedral : 6.356 87.627 4392 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.50 % Allowed : 10.47 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.94 (0.14), residues: 3804 helix: 2.09 (0.10), residues: 2472 sheet: 0.16 (0.36), residues: 284 loop : -0.28 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 113 TYR 0.015 0.001 TYR C 227 PHE 0.013 0.001 PHE B 975 TRP 0.011 0.001 TRP B1124 HIS 0.005 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00322 (31696) covalent geometry : angle 0.49733 (42984) hydrogen bonds : bond 0.04056 ( 1868) hydrogen bonds : angle 4.28791 ( 5496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 301 time to evaluate : 1.311 Fit side-chains REVERT: B 132 THR cc_start: 0.8020 (m) cc_final: 0.7810 (t) REVERT: B 140 ARG cc_start: 0.8363 (mmt180) cc_final: 0.8077 (mmt-90) REVERT: B 202 ASN cc_start: 0.8115 (t0) cc_final: 0.7854 (t0) REVERT: B 204 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7670 (mtpp) REVERT: B 210 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7243 (mtm110) REVERT: B 284 MET cc_start: 0.7932 (tpp) cc_final: 0.7566 (mmp) REVERT: B 289 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: B 293 GLN cc_start: 0.7743 (tt0) cc_final: 0.7165 (mm110) REVERT: B 475 ASN cc_start: 0.7420 (t0) cc_final: 0.7172 (t0) REVERT: B 505 HIS cc_start: 0.7398 (m90) cc_final: 0.6791 (t70) REVERT: B 635 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7545 (mp0) REVERT: B 662 ASP cc_start: 0.8045 (m-30) cc_final: 0.7634 (t70) REVERT: B 695 LEU cc_start: 0.8358 (mt) cc_final: 0.7814 (tp) REVERT: B 769 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6938 (mm) REVERT: B 915 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6676 (mm-40) REVERT: B 1053 ASN cc_start: 0.8446 (m110) cc_final: 0.8035 (m-40) REVERT: B 1116 GLU cc_start: 0.7560 (mp0) cc_final: 0.7244 (tm-30) REVERT: A 140 ARG cc_start: 0.8377 (mmt180) cc_final: 0.8092 (mmt-90) REVERT: A 202 ASN cc_start: 0.8105 (t0) cc_final: 0.7846 (t0) REVERT: A 204 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7655 (mtpp) REVERT: A 210 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7250 (mtm110) REVERT: A 284 MET cc_start: 0.7918 (tpp) cc_final: 0.7548 (mmp) REVERT: A 289 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: A 293 GLN cc_start: 0.7742 (tt0) cc_final: 0.7172 (mm110) REVERT: A 371 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 475 ASN cc_start: 0.7398 (t0) cc_final: 0.7149 (t0) REVERT: A 505 HIS cc_start: 0.7398 (m90) cc_final: 0.6796 (t70) REVERT: A 635 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7545 (mp0) REVERT: A 662 ASP cc_start: 0.8034 (m-30) cc_final: 0.7642 (t70) REVERT: A 695 LEU cc_start: 0.8352 (mt) cc_final: 0.7812 (tp) REVERT: A 769 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6941 (mm) REVERT: A 915 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6684 (mm-40) REVERT: A 1053 ASN cc_start: 0.8405 (m110) cc_final: 0.7997 (m-40) REVERT: A 1116 GLU cc_start: 0.7550 (mp0) cc_final: 0.7246 (tm-30) REVERT: C 132 THR cc_start: 0.8024 (m) cc_final: 0.7816 (t) REVERT: C 140 ARG cc_start: 0.8386 (mmt180) cc_final: 0.8098 (mmt-90) REVERT: C 202 ASN cc_start: 0.8104 (t0) cc_final: 0.7844 (t0) REVERT: C 204 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7655 (mtpp) REVERT: C 210 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7229 (mtm110) REVERT: C 284 MET cc_start: 0.7923 (tpp) cc_final: 0.7554 (mmp) REVERT: C 289 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: C 293 GLN cc_start: 0.7749 (tt0) cc_final: 0.7180 (mm110) REVERT: C 475 ASN cc_start: 0.7408 (t0) cc_final: 0.7158 (t0) REVERT: C 505 HIS cc_start: 0.7416 (m90) cc_final: 0.6816 (t70) REVERT: C 635 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7538 (mp0) REVERT: C 662 ASP cc_start: 0.8029 (m-30) cc_final: 0.7634 (t70) REVERT: C 695 LEU cc_start: 0.8353 (mt) cc_final: 0.7811 (tp) REVERT: C 769 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6942 (mm) REVERT: C 915 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6680 (mm-40) REVERT: C 1053 ASN cc_start: 0.8428 (m110) cc_final: 0.8015 (m-40) REVERT: C 1116 GLU cc_start: 0.7538 (mp0) cc_final: 0.7262 (tm-30) REVERT: D 132 THR cc_start: 0.8008 (m) cc_final: 0.7791 (t) REVERT: D 140 ARG cc_start: 0.8367 (mmt180) cc_final: 0.8075 (mmt-90) REVERT: D 202 ASN cc_start: 0.8109 (t0) cc_final: 0.7846 (t0) REVERT: D 204 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7657 (mtpp) REVERT: D 210 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7214 (mtm110) REVERT: D 284 MET cc_start: 0.7928 (tpp) cc_final: 0.7558 (mmp) REVERT: D 289 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: D 293 GLN cc_start: 0.7738 (tt0) cc_final: 0.7181 (mm110) REVERT: D 475 ASN cc_start: 0.7434 (t0) cc_final: 0.7195 (t0) REVERT: D 505 HIS cc_start: 0.7398 (m90) cc_final: 0.6793 (t70) REVERT: D 635 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7540 (mp0) REVERT: D 662 ASP cc_start: 0.8020 (m-30) cc_final: 0.7624 (t70) REVERT: D 695 LEU cc_start: 0.8347 (mt) cc_final: 0.7805 (tp) REVERT: D 769 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6949 (mm) REVERT: D 915 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6695 (mm-40) REVERT: D 1053 ASN cc_start: 0.8427 (m110) cc_final: 0.8012 (m-40) REVERT: D 1116 GLU cc_start: 0.7571 (mp0) cc_final: 0.7245 (tm-30) outliers start: 82 outliers final: 30 residues processed: 354 average time/residue: 0.7242 time to fit residues: 300.8817 Evaluate side-chains 337 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 306 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN A 66 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN C 66 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1014 GLN D 66 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118923 restraints weight = 34797.861| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.99 r_work: 0.3212 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31696 Z= 0.135 Angle : 0.502 9.663 42984 Z= 0.255 Chirality : 0.037 0.168 4796 Planarity : 0.004 0.064 5412 Dihedral : 6.298 87.281 4392 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 10.71 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.96 (0.14), residues: 3804 helix: 2.10 (0.10), residues: 2472 sheet: 0.13 (0.36), residues: 284 loop : -0.24 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 113 TYR 0.014 0.001 TYR C 227 PHE 0.012 0.001 PHE A 975 TRP 0.011 0.001 TRP B1124 HIS 0.005 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00316 (31696) covalent geometry : angle 0.50186 (42984) hydrogen bonds : bond 0.04043 ( 1868) hydrogen bonds : angle 4.26967 ( 5496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 298 time to evaluate : 1.231 Fit side-chains REVERT: B 132 THR cc_start: 0.8038 (m) cc_final: 0.7810 (t) REVERT: B 140 ARG cc_start: 0.8388 (mmt180) cc_final: 0.8103 (mmt-90) REVERT: B 202 ASN cc_start: 0.8087 (t0) cc_final: 0.7818 (t0) REVERT: B 204 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7277 (mtpp) REVERT: B 210 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7251 (mtm110) REVERT: B 284 MET cc_start: 0.7915 (tpp) cc_final: 0.7557 (mmp) REVERT: B 289 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: B 293 GLN cc_start: 0.7803 (tt0) cc_final: 0.7189 (mm110) REVERT: B 475 ASN cc_start: 0.7413 (t0) cc_final: 0.7155 (t0) REVERT: B 505 HIS cc_start: 0.7441 (m90) cc_final: 0.6793 (t70) REVERT: B 635 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7587 (mp0) REVERT: B 662 ASP cc_start: 0.8139 (m-30) cc_final: 0.7679 (t70) REVERT: B 695 LEU cc_start: 0.8342 (mt) cc_final: 0.7794 (tp) REVERT: B 769 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6913 (mm) REVERT: B 915 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6752 (mm-40) REVERT: B 1053 ASN cc_start: 0.8510 (m110) cc_final: 0.8089 (m-40) REVERT: A 140 ARG cc_start: 0.8420 (mmt180) cc_final: 0.8136 (mmt-90) REVERT: A 202 ASN cc_start: 0.8082 (t0) cc_final: 0.7818 (t0) REVERT: A 204 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7280 (mtpp) REVERT: A 210 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7265 (mtm110) REVERT: A 284 MET cc_start: 0.7899 (tpp) cc_final: 0.7541 (mmp) REVERT: A 289 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: A 293 GLN cc_start: 0.7810 (tt0) cc_final: 0.7207 (mm110) REVERT: A 371 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: A 475 ASN cc_start: 0.7390 (t0) cc_final: 0.7130 (t0) REVERT: A 505 HIS cc_start: 0.7429 (m90) cc_final: 0.6794 (t70) REVERT: A 635 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7587 (mp0) REVERT: A 662 ASP cc_start: 0.8123 (m-30) cc_final: 0.7678 (t70) REVERT: A 695 LEU cc_start: 0.8342 (mt) cc_final: 0.7792 (tp) REVERT: A 769 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6919 (mm) REVERT: A 915 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6759 (mm-40) REVERT: A 1053 ASN cc_start: 0.8472 (m110) cc_final: 0.8055 (m-40) REVERT: C 132 THR cc_start: 0.8034 (m) cc_final: 0.7810 (t) REVERT: C 140 ARG cc_start: 0.8420 (mmt180) cc_final: 0.8135 (mmt-90) REVERT: C 202 ASN cc_start: 0.8076 (t0) cc_final: 0.7808 (t0) REVERT: C 204 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7277 (mtpp) REVERT: C 210 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7255 (mtm110) REVERT: C 284 MET cc_start: 0.7906 (tpp) cc_final: 0.7547 (mmp) REVERT: C 289 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: C 293 GLN cc_start: 0.7828 (tt0) cc_final: 0.7213 (mm110) REVERT: C 475 ASN cc_start: 0.7388 (t0) cc_final: 0.7122 (t0) REVERT: C 505 HIS cc_start: 0.7444 (m90) cc_final: 0.6801 (t70) REVERT: C 635 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7579 (mp0) REVERT: C 662 ASP cc_start: 0.8129 (m-30) cc_final: 0.7678 (t70) REVERT: C 695 LEU cc_start: 0.8340 (mt) cc_final: 0.7790 (tp) REVERT: C 769 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6917 (mm) REVERT: C 915 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6746 (mm-40) REVERT: C 1053 ASN cc_start: 0.8477 (m110) cc_final: 0.8057 (m-40) REVERT: D 132 THR cc_start: 0.8014 (m) cc_final: 0.7778 (t) REVERT: D 140 ARG cc_start: 0.8396 (mmt180) cc_final: 0.8104 (mmt-90) REVERT: D 202 ASN cc_start: 0.8079 (t0) cc_final: 0.7808 (t0) REVERT: D 204 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7266 (mtpp) REVERT: D 210 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7231 (mtm110) REVERT: D 284 MET cc_start: 0.7912 (tpp) cc_final: 0.7551 (mmp) REVERT: D 289 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: D 293 GLN cc_start: 0.7812 (tt0) cc_final: 0.7211 (mm110) REVERT: D 475 ASN cc_start: 0.7433 (t0) cc_final: 0.7165 (t0) REVERT: D 505 HIS cc_start: 0.7425 (m90) cc_final: 0.6784 (t70) REVERT: D 635 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7573 (mp0) REVERT: D 662 ASP cc_start: 0.8115 (m-30) cc_final: 0.7666 (t70) REVERT: D 695 LEU cc_start: 0.8333 (mt) cc_final: 0.7787 (tp) REVERT: D 769 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6921 (mm) REVERT: D 915 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6755 (mm-40) REVERT: D 1053 ASN cc_start: 0.8471 (m110) cc_final: 0.8051 (m-40) outliers start: 77 outliers final: 34 residues processed: 351 average time/residue: 0.7361 time to fit residues: 300.8833 Evaluate side-chains 342 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 133 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 283 optimal weight: 0.0970 chunk 29 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 348 GLN B1014 GLN A 66 HIS A 348 GLN A1014 GLN C 66 HIS C 348 GLN C1014 GLN D 66 HIS D 348 GLN D1014 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120370 restraints weight = 35061.378| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.92 r_work: 0.3241 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31696 Z= 0.120 Angle : 0.487 10.277 42984 Z= 0.246 Chirality : 0.036 0.160 4796 Planarity : 0.004 0.061 5412 Dihedral : 6.177 86.724 4392 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.29 % Allowed : 11.02 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.14), residues: 3804 helix: 2.20 (0.10), residues: 2472 sheet: 0.15 (0.36), residues: 284 loop : -0.20 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 113 TYR 0.013 0.001 TYR D 227 PHE 0.011 0.001 PHE A 627 TRP 0.012 0.001 TRP A1124 HIS 0.004 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00273 (31696) covalent geometry : angle 0.48734 (42984) hydrogen bonds : bond 0.03825 ( 1868) hydrogen bonds : angle 4.21059 ( 5496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 315 time to evaluate : 1.025 Fit side-chains REVERT: B 132 THR cc_start: 0.8017 (m) cc_final: 0.7806 (t) REVERT: B 140 ARG cc_start: 0.8358 (mmt180) cc_final: 0.8073 (mmt-90) REVERT: B 202 ASN cc_start: 0.8099 (t0) cc_final: 0.7839 (t0) REVERT: B 204 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7656 (mtpp) REVERT: B 210 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7306 (mtm110) REVERT: B 284 MET cc_start: 0.7889 (tpp) cc_final: 0.7537 (mmp) REVERT: B 289 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: B 293 GLN cc_start: 0.7807 (tt0) cc_final: 0.7227 (mm110) REVERT: B 475 ASN cc_start: 0.7385 (t0) cc_final: 0.7084 (t0) REVERT: B 505 HIS cc_start: 0.7404 (m90) cc_final: 0.6801 (t70) REVERT: B 635 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7550 (mp0) REVERT: B 662 ASP cc_start: 0.8124 (m-30) cc_final: 0.7681 (t0) REVERT: B 695 LEU cc_start: 0.8337 (mt) cc_final: 0.7785 (tp) REVERT: B 769 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6937 (mm) REVERT: B 915 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6718 (mm-40) REVERT: B 1053 ASN cc_start: 0.8451 (m110) cc_final: 0.8038 (m-40) REVERT: B 1116 GLU cc_start: 0.7545 (mp0) cc_final: 0.7223 (tm-30) REVERT: A 140 ARG cc_start: 0.8380 (mmt180) cc_final: 0.8092 (mmt-90) REVERT: A 202 ASN cc_start: 0.8106 (t0) cc_final: 0.7849 (t0) REVERT: A 204 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7650 (mtpp) REVERT: A 210 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7328 (mtm110) REVERT: A 284 MET cc_start: 0.7884 (tpp) cc_final: 0.7529 (mmp) REVERT: A 289 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 293 GLN cc_start: 0.7812 (tt0) cc_final: 0.7242 (mm110) REVERT: A 371 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: A 475 ASN cc_start: 0.7367 (t0) cc_final: 0.7065 (t0) REVERT: A 505 HIS cc_start: 0.7410 (m90) cc_final: 0.6813 (t70) REVERT: A 635 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7570 (mp0) REVERT: A 662 ASP cc_start: 0.8102 (m-30) cc_final: 0.7679 (t0) REVERT: A 695 LEU cc_start: 0.8328 (mt) cc_final: 0.7773 (tp) REVERT: A 769 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6947 (mm) REVERT: A 915 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6712 (mm-40) REVERT: A 1053 ASN cc_start: 0.8431 (m110) cc_final: 0.8018 (m-40) REVERT: A 1116 GLU cc_start: 0.7530 (mp0) cc_final: 0.7235 (tm-30) REVERT: C 132 THR cc_start: 0.8022 (m) cc_final: 0.7814 (t) REVERT: C 140 ARG cc_start: 0.8364 (mmt180) cc_final: 0.8072 (mmt-90) REVERT: C 202 ASN cc_start: 0.8096 (t0) cc_final: 0.7837 (t0) REVERT: C 204 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7643 (mtpp) REVERT: C 210 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7309 (mtm110) REVERT: C 284 MET cc_start: 0.7901 (tpp) cc_final: 0.7542 (mmp) REVERT: C 289 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: C 293 GLN cc_start: 0.7827 (tt0) cc_final: 0.7253 (mm110) REVERT: C 475 ASN cc_start: 0.7367 (t0) cc_final: 0.7060 (t0) REVERT: C 505 HIS cc_start: 0.7420 (m90) cc_final: 0.6817 (t70) REVERT: C 635 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7546 (mp0) REVERT: C 662 ASP cc_start: 0.8108 (m-30) cc_final: 0.7682 (t0) REVERT: C 695 LEU cc_start: 0.8328 (mt) cc_final: 0.7768 (tp) REVERT: C 769 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6943 (mm) REVERT: C 915 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6718 (mm-40) REVERT: C 1053 ASN cc_start: 0.8416 (m110) cc_final: 0.8001 (m-40) REVERT: C 1116 GLU cc_start: 0.7521 (mp0) cc_final: 0.7246 (tm-30) REVERT: D 132 THR cc_start: 0.8005 (m) cc_final: 0.7794 (t) REVERT: D 140 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8080 (mmt-90) REVERT: D 202 ASN cc_start: 0.8087 (t0) cc_final: 0.7826 (t0) REVERT: D 204 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7645 (mtpp) REVERT: D 210 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7296 (mtm110) REVERT: D 284 MET cc_start: 0.7897 (tpp) cc_final: 0.7544 (mmp) REVERT: D 289 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: D 293 GLN cc_start: 0.7832 (tt0) cc_final: 0.7247 (mm110) REVERT: D 475 ASN cc_start: 0.7400 (t0) cc_final: 0.7113 (t0) REVERT: D 505 HIS cc_start: 0.7411 (m90) cc_final: 0.6801 (t70) REVERT: D 635 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7548 (mp0) REVERT: D 662 ASP cc_start: 0.8099 (m-30) cc_final: 0.7666 (t0) REVERT: D 695 LEU cc_start: 0.8320 (mt) cc_final: 0.7762 (tp) REVERT: D 769 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6957 (mm) REVERT: D 915 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6718 (mm-40) REVERT: D 1053 ASN cc_start: 0.8432 (m110) cc_final: 0.8017 (m-40) REVERT: D 1116 GLU cc_start: 0.7561 (mp0) cc_final: 0.7226 (tm-30) outliers start: 75 outliers final: 34 residues processed: 364 average time/residue: 0.7115 time to fit residues: 302.5866 Evaluate side-chains 355 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 300 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 993 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 10 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 214 optimal weight: 0.0770 chunk 287 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 259 GLN B 348 GLN B1014 GLN A 66 HIS A 259 GLN A 348 GLN A1014 GLN C 66 HIS C 259 GLN C 348 GLN C1014 GLN D 66 HIS D 259 GLN D 348 GLN D1014 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.166014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119323 restraints weight = 34625.816| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.90 r_work: 0.3244 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31696 Z= 0.144 Angle : 0.518 12.132 42984 Z= 0.259 Chirality : 0.037 0.171 4796 Planarity : 0.004 0.061 5412 Dihedral : 6.181 85.696 4392 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.23 % Allowed : 11.20 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.14), residues: 3804 helix: 2.13 (0.10), residues: 2472 sheet: 0.16 (0.36), residues: 284 loop : -0.22 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 905 TYR 0.015 0.001 TYR C 227 PHE 0.013 0.001 PHE A 975 TRP 0.011 0.001 TRP D1124 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00339 (31696) covalent geometry : angle 0.51799 (42984) hydrogen bonds : bond 0.04144 ( 1868) hydrogen bonds : angle 4.26877 ( 5496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 1.230 Fit side-chains REVERT: B 132 THR cc_start: 0.8043 (m) cc_final: 0.7818 (t) REVERT: B 140 ARG cc_start: 0.8380 (mmt180) cc_final: 0.8096 (mmt-90) REVERT: B 202 ASN cc_start: 0.8130 (t0) cc_final: 0.7877 (t0) REVERT: B 210 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7334 (mtm110) REVERT: B 284 MET cc_start: 0.7898 (tpp) cc_final: 0.7537 (mmp) REVERT: B 289 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: B 293 GLN cc_start: 0.7828 (tt0) cc_final: 0.7246 (mm110) REVERT: B 475 ASN cc_start: 0.7424 (t0) cc_final: 0.7167 (t0) REVERT: B 505 HIS cc_start: 0.7407 (m90) cc_final: 0.6838 (t70) REVERT: B 635 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7565 (mp0) REVERT: B 662 ASP cc_start: 0.8062 (m-30) cc_final: 0.7656 (t70) REVERT: B 695 LEU cc_start: 0.8362 (mt) cc_final: 0.7805 (tp) REVERT: B 769 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6911 (mm) REVERT: B 915 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6721 (mm-40) REVERT: B 1053 ASN cc_start: 0.8457 (m110) cc_final: 0.8046 (m-40) REVERT: A 140 ARG cc_start: 0.8402 (mmt180) cc_final: 0.8114 (mmt-90) REVERT: A 202 ASN cc_start: 0.8131 (t0) cc_final: 0.7880 (t0) REVERT: A 210 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7345 (mtm110) REVERT: A 284 MET cc_start: 0.7897 (tpp) cc_final: 0.7532 (mmp) REVERT: A 289 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: A 293 GLN cc_start: 0.7830 (tt0) cc_final: 0.7264 (mm110) REVERT: A 371 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 475 ASN cc_start: 0.7383 (t0) cc_final: 0.7123 (t0) REVERT: A 505 HIS cc_start: 0.7399 (m90) cc_final: 0.6836 (t70) REVERT: A 635 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7571 (mp0) REVERT: A 662 ASP cc_start: 0.8048 (m-30) cc_final: 0.7660 (t70) REVERT: A 695 LEU cc_start: 0.8347 (mt) cc_final: 0.7798 (tp) REVERT: A 769 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6916 (mm) REVERT: A 915 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6716 (mm-40) REVERT: A 1053 ASN cc_start: 0.8428 (m110) cc_final: 0.8018 (m-40) REVERT: C 132 THR cc_start: 0.8037 (m) cc_final: 0.7821 (t) REVERT: C 140 ARG cc_start: 0.8388 (mmt180) cc_final: 0.8097 (mmt-90) REVERT: C 202 ASN cc_start: 0.8126 (t0) cc_final: 0.7876 (t0) REVERT: C 210 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7325 (mtm110) REVERT: C 284 MET cc_start: 0.7907 (tpp) cc_final: 0.7539 (mmp) REVERT: C 289 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: C 293 GLN cc_start: 0.7848 (tt0) cc_final: 0.7270 (mm110) REVERT: C 475 ASN cc_start: 0.7368 (t0) cc_final: 0.7104 (t0) REVERT: C 505 HIS cc_start: 0.7414 (m90) cc_final: 0.6844 (t70) REVERT: C 635 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7559 (mp0) REVERT: C 662 ASP cc_start: 0.8057 (m-30) cc_final: 0.7655 (t70) REVERT: C 695 LEU cc_start: 0.8349 (mt) cc_final: 0.7795 (tp) REVERT: C 769 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6912 (mm) REVERT: C 915 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6717 (mm-40) REVERT: C 1053 ASN cc_start: 0.8433 (m110) cc_final: 0.8021 (m-40) REVERT: D 132 THR cc_start: 0.8023 (m) cc_final: 0.7797 (t) REVERT: D 140 ARG cc_start: 0.8391 (mmt180) cc_final: 0.8101 (mmt-90) REVERT: D 202 ASN cc_start: 0.8125 (t0) cc_final: 0.7873 (t0) REVERT: D 210 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7327 (mtm110) REVERT: D 284 MET cc_start: 0.7897 (tpp) cc_final: 0.7534 (mmp) REVERT: D 289 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: D 293 GLN cc_start: 0.7832 (tt0) cc_final: 0.7256 (mm110) REVERT: D 371 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: D 475 ASN cc_start: 0.7418 (t0) cc_final: 0.7154 (t0) REVERT: D 505 HIS cc_start: 0.7401 (m90) cc_final: 0.6834 (t70) REVERT: D 635 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7552 (mp0) REVERT: D 662 ASP cc_start: 0.8052 (m-30) cc_final: 0.7650 (t70) REVERT: D 695 LEU cc_start: 0.8338 (mt) cc_final: 0.7789 (tp) REVERT: D 769 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6918 (mm) REVERT: D 915 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6721 (mm-40) REVERT: D 1053 ASN cc_start: 0.8441 (m110) cc_final: 0.8029 (m-40) outliers start: 73 outliers final: 32 residues processed: 347 average time/residue: 0.6929 time to fit residues: 283.0815 Evaluate side-chains 344 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 915 GLN Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 993 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 66 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 345 optimal weight: 0.3980 chunk 188 optimal weight: 4.9990 chunk 340 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 321 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 348 GLN B1014 GLN A 66 HIS A 348 GLN A1014 GLN C 66 HIS C 348 GLN C1014 GLN D 66 HIS D 348 GLN D1014 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119697 restraints weight = 34759.776| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.91 r_work: 0.3241 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31696 Z= 0.133 Angle : 0.515 14.161 42984 Z= 0.257 Chirality : 0.036 0.166 4796 Planarity : 0.004 0.061 5412 Dihedral : 6.149 85.974 4392 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.77 % Allowed : 11.84 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.14), residues: 3804 helix: 2.18 (0.10), residues: 2472 sheet: 0.09 (0.36), residues: 276 loop : -0.21 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 905 TYR 0.014 0.001 TYR D 227 PHE 0.012 0.001 PHE C 975 TRP 0.011 0.001 TRP A1124 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00311 (31696) covalent geometry : angle 0.51470 (42984) hydrogen bonds : bond 0.03994 ( 1868) hydrogen bonds : angle 4.24264 ( 5496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13433.34 seconds wall clock time: 228 minutes 29.76 seconds (13709.76 seconds total)