Starting phenix.real_space_refine on Tue May 27 21:20:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b90_44364/05_2025/9b90_44364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b90_44364/05_2025/9b90_44364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b90_44364/05_2025/9b90_44364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b90_44364/05_2025/9b90_44364.map" model { file = "/net/cci-nas-00/data/ceres_data/9b90_44364/05_2025/9b90_44364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b90_44364/05_2025/9b90_44364.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.013 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 12 5.49 5 S 152 5.16 5 C 19220 2.51 5 N 5228 2.21 5 O 5100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7397 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 42, 'TRANS': 939} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 298 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, B, D Time building chain proxies: 20.16, per 1000 atoms: 0.68 Number of scatterers: 29720 At special positions: 0 Unit cell: (169.74, 169.74, 152.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 152 16.00 P 12 15.00 O 5100 8.00 N 5228 7.00 C 19220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.89 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.89 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.89 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.88 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: 8.23 Conformation dependent library (CDL) restraints added in 3.8 seconds 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 16 sheets defined 68.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 645 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 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 767 through 778 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 862 removed outlier: 3.646A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 973 Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1176 Processing helix chain 'A' and resid 1177 through 1177 No H-bonds generated for 'chain 'A' and resid 1177 through 1177' Processing helix chain 'B' and resid 7 through 8 No H-bonds generated for 'chain 'B' and resid 7 through 8' Processing helix chain 'B' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.606A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 421 through 436 removed outlier: 4.142A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.649A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 603 Processing helix chain 'B' and resid 607 through 634 Processing helix chain 'B' and resid 634 through 645 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 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 767 through 778 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 862 removed outlier: 3.645A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 906 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 916 through 926 Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 973 Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1176 Processing helix chain 'B' and resid 1177 through 1177 No H-bonds generated for 'chain 'B' and resid 1177 through 1177' Processing helix chain 'C' and resid 7 through 8 No H-bonds generated for 'chain 'C' and resid 7 through 8' Processing helix chain 'C' and resid 9 through 15 removed outlier: 4.167A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 603 Processing helix chain 'C' and resid 607 through 634 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 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 767 through 778 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 862 removed outlier: 3.646A pdb=" N ASP C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 906 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 916 through 926 Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 973 Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C1082 " --> pdb=" O PRO C1078 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1176 Processing helix chain 'C' and resid 1177 through 1177 No H-bonds generated for 'chain 'C' and resid 1177 through 1177' Processing helix chain 'D' and resid 7 through 8 No H-bonds generated for 'chain 'D' and resid 7 through 8' Processing helix chain 'D' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.724A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.983A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY D 386 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 603 Processing helix chain 'D' and resid 607 through 634 Processing helix chain 'D' and resid 634 through 645 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 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 767 through 778 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 862 removed outlier: 3.646A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 906 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 973 Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.768A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1088 removed outlier: 4.129A pdb=" N VAL D1081 " --> pdb=" O PRO D1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE D1082 " --> pdb=" O PRO D1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1176 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 7.998A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A 156 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE A 269 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR B 211 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY B 156 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE B 269 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'C' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR C 211 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY C 156 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 261 through 262 removed outlier: 3.956A pdb=" N ILE C 269 " --> pdb=" O THR C 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.173A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'D' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR D 211 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY D 156 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE D 269 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1936 hydrogen bonds defined for protein. 5616 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: 12.26 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9608 1.34 - 1.46: 7133 1.46 - 1.58: 13403 1.58 - 1.69: 20 1.69 - 1.81: 228 Bond restraints: 30392 Sorted by residual: bond pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 1.541 1.529 0.012 1.20e-02 6.94e+03 1.04e+00 bond pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 9.06e-01 bond pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 8.62e-01 bond pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 8.38e-01 bond pdb=" CB TRP C1124 " pdb=" CG TRP C1124 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.57e-01 ... (remaining 30387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 40631 1.29 - 2.57: 537 2.57 - 3.86: 148 3.86 - 5.15: 48 5.15 - 6.43: 20 Bond angle restraints: 41384 Sorted by residual: angle pdb=" N GLU A 371 " pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N GLU C 371 " pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 114.17 110.49 3.68 1.14e+00 7.69e-01 1.04e+01 angle pdb=" N GLU B 371 " pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N GLU D 371 " pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" C3' ATP D2003 " pdb=" C4' ATP D2003 " pdb=" C5' ATP D2003 " ideal model delta sigma weight residual 115.19 111.00 4.19 1.76e+00 3.23e-01 5.66e+00 ... (remaining 41379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 17023 16.76 - 33.51: 665 33.51 - 50.27: 152 50.27 - 67.03: 40 67.03 - 83.79: 20 Dihedral angle restraints: 17900 sinusoidal: 6628 harmonic: 11272 Sorted by residual: dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N PRO B 208 " pdb=" CA PRO B 208 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 17897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4395 0.059 - 0.118: 361 0.118 - 0.177: 20 0.177 - 0.236: 0 0.236 - 0.294: 12 Chirality restraints: 4788 Sorted by residual: chirality pdb=" C2' ATP B2003 " pdb=" C1' ATP B2003 " pdb=" C3' ATP B2003 " pdb=" O2' ATP B2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP A2003 " pdb=" C1' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" O2' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP D2003 " pdb=" C1' ATP D2003 " pdb=" C3' ATP D2003 " pdb=" O2' ATP D2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4785 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 437 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 438 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 437 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO B 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 437 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 438 " 0.018 5.00e-02 4.00e+02 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 851 2.70 - 3.25: 34325 3.25 - 3.80: 50589 3.80 - 4.35: 58847 4.35 - 4.90: 99939 Nonbonded interactions: 244551 Sorted by model distance: nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.154 2.510 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.154 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.154 2.510 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.154 2.510 nonbonded pdb=" OE1 GLN C 831 " pdb="CA CA C2001 " model vdw 2.184 2.510 ... (remaining 244546 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.230 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 69.320 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.855 30396 Z= 0.523 Angle : 0.554 28.602 41392 Z= 0.291 Chirality : 0.035 0.294 4788 Planarity : 0.003 0.031 5196 Dihedral : 10.679 83.785 10592 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3848 helix: 1.66 (0.10), residues: 2440 sheet: -1.03 (0.35), residues: 244 loop : 0.01 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 776 HIS 0.002 0.001 HIS D1070 PHE 0.006 0.001 PHE B1069 TYR 0.005 0.001 TYR B 968 ARG 0.003 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.19497 ( 1936) hydrogen bonds : angle 7.37161 ( 5616) SS BOND : bond 0.85409 ( 4) SS BOND : angle 21.29922 ( 8) covalent geometry : bond 0.00376 (30392) covalent geometry : angle 0.46791 (41384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 274 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1034 LEU cc_start: 0.9170 (mp) cc_final: 0.8893 (tp) REVERT: B 1034 LEU cc_start: 0.9136 (mp) cc_final: 0.8831 (tp) REVERT: C 1034 LEU cc_start: 0.9099 (mp) cc_final: 0.8819 (tp) REVERT: D 1034 LEU cc_start: 0.9151 (mp) cc_final: 0.8863 (tp) outliers start: 12 outliers final: 8 residues processed: 286 average time/residue: 0.4055 time to fit residues: 187.1702 Evaluate side-chains 205 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 0.0050 chunk 200 optimal weight: 0.0370 chunk 158 optimal weight: 8.9990 chunk 307 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 355 optimal weight: 9.9990 overall best weight: 3.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 410 GLN A 505 HIS A 973 GLN B 165 HIS B 410 GLN B 505 HIS B 973 GLN C 165 HIS C 410 GLN C 505 HIS C 973 GLN D 165 HIS D 410 GLN D 505 HIS D 973 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.074129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054732 restraints weight = 140072.846| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.87 r_work: 0.2696 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30396 Z= 0.206 Angle : 0.604 10.470 41392 Z= 0.306 Chirality : 0.038 0.161 4788 Planarity : 0.004 0.042 5196 Dihedral : 7.563 86.262 4368 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.67 % Allowed : 8.11 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3848 helix: 2.56 (0.10), residues: 2476 sheet: -1.03 (0.37), residues: 244 loop : 0.20 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1058 HIS 0.008 0.001 HIS C 505 PHE 0.019 0.001 PHE B 373 TYR 0.007 0.001 TYR D 227 ARG 0.006 0.001 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 1936) hydrogen bonds : angle 4.88254 ( 5616) SS BOND : bond 0.00275 ( 4) SS BOND : angle 2.35170 ( 8) covalent geometry : bond 0.00458 (30392) covalent geometry : angle 0.60309 (41384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9362 (tpp) cc_final: 0.8933 (mmm) REVERT: A 669 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 930 VAL cc_start: 0.9248 (t) cc_final: 0.8972 (p) REVERT: A 1034 LEU cc_start: 0.9324 (mp) cc_final: 0.9028 (tp) REVERT: A 1037 ASN cc_start: 0.9533 (m-40) cc_final: 0.9309 (m110) REVERT: B 477 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9266 (mm) REVERT: B 576 MET cc_start: 0.9188 (mmm) cc_final: 0.8797 (mmm) REVERT: B 599 MET cc_start: 0.9122 (ttm) cc_final: 0.8917 (ttm) REVERT: B 669 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8197 (tm-30) REVERT: B 951 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9288 (mp) REVERT: B 1034 LEU cc_start: 0.9272 (mp) cc_final: 0.8977 (tp) REVERT: B 1146 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8855 (mp0) REVERT: C 477 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9270 (mm) REVERT: C 576 MET cc_start: 0.9169 (mmm) cc_final: 0.8793 (mmm) REVERT: C 660 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.9078 (mt0) REVERT: C 669 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 951 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9297 (mp) REVERT: C 1034 LEU cc_start: 0.9268 (mp) cc_final: 0.8993 (tp) REVERT: C 1146 GLU cc_start: 0.9401 (mm-30) cc_final: 0.8811 (mp0) REVERT: D 175 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.9300 (mtp) REVERT: D 477 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9253 (mm) REVERT: D 576 MET cc_start: 0.9227 (mmm) cc_final: 0.8647 (mmm) REVERT: D 669 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8285 (tm-30) REVERT: D 951 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9317 (mp) REVERT: D 1034 LEU cc_start: 0.9322 (mp) cc_final: 0.8994 (tp) REVERT: D 1037 ASN cc_start: 0.9508 (m-40) cc_final: 0.9280 (m110) REVERT: D 1146 GLU cc_start: 0.9388 (mm-30) cc_final: 0.8784 (mp0) outliers start: 48 outliers final: 14 residues processed: 281 average time/residue: 0.3901 time to fit residues: 180.2356 Evaluate side-chains 224 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 237 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 373 optimal weight: 0.0060 chunk 279 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 250 optimal weight: 0.1980 chunk 112 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 overall best weight: 2.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 410 GLN B 165 HIS B 410 GLN C 165 HIS C 410 GLN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS D 410 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.074629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055320 restraints weight = 138011.950| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.86 r_work: 0.2707 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30396 Z= 0.155 Angle : 0.540 9.553 41392 Z= 0.275 Chirality : 0.037 0.158 4788 Planarity : 0.004 0.045 5196 Dihedral : 7.143 86.280 4364 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.85 % Allowed : 9.37 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.14), residues: 3848 helix: 2.54 (0.10), residues: 2480 sheet: -1.02 (0.37), residues: 244 loop : 0.19 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.004 0.001 HIS B1128 PHE 0.012 0.001 PHE A 627 TYR 0.008 0.001 TYR D 227 ARG 0.007 0.000 ARG B1138 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 1936) hydrogen bonds : angle 4.62596 ( 5616) SS BOND : bond 0.00460 ( 4) SS BOND : angle 1.33824 ( 8) covalent geometry : bond 0.00344 (30392) covalent geometry : angle 0.53943 (41384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.9596 (tpp) cc_final: 0.9154 (mmm) REVERT: A 576 MET cc_start: 0.9407 (tpp) cc_final: 0.9007 (mmm) REVERT: A 622 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8910 (ttm) REVERT: A 930 VAL cc_start: 0.9218 (t) cc_final: 0.8970 (p) REVERT: A 951 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9261 (mp) REVERT: A 1034 LEU cc_start: 0.9327 (mp) cc_final: 0.9032 (tp) REVERT: A 1037 ASN cc_start: 0.9531 (m-40) cc_final: 0.9327 (m110) REVERT: A 1125 GLU cc_start: 0.9356 (tt0) cc_final: 0.9146 (tm-30) REVERT: B 430 MET cc_start: 0.9613 (tpp) cc_final: 0.9045 (mmm) REVERT: B 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9250 (mm) REVERT: B 576 MET cc_start: 0.9240 (mmm) cc_final: 0.8764 (mmm) REVERT: B 599 MET cc_start: 0.9160 (ttm) cc_final: 0.8697 (ttm) REVERT: B 669 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8175 (tm-30) REVERT: B 951 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9329 (mp) REVERT: B 1034 LEU cc_start: 0.9220 (mp) cc_final: 0.8915 (tp) REVERT: B 1146 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8943 (mp0) REVERT: C 477 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9251 (mm) REVERT: C 576 MET cc_start: 0.9308 (mmm) cc_final: 0.8893 (mmm) REVERT: C 580 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8952 (mt-10) REVERT: C 599 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8600 (ttm) REVERT: C 660 GLN cc_start: 0.9530 (OUTLIER) cc_final: 0.9052 (mt0) REVERT: C 669 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 951 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9311 (mp) REVERT: C 1034 LEU cc_start: 0.9222 (mp) cc_final: 0.8952 (tp) REVERT: C 1146 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8867 (mp0) REVERT: D 430 MET cc_start: 0.9621 (tpp) cc_final: 0.9209 (mmm) REVERT: D 477 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9245 (mm) REVERT: D 576 MET cc_start: 0.9352 (mmm) cc_final: 0.9006 (mmm) REVERT: D 580 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8952 (mt-10) REVERT: D 951 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9323 (mp) REVERT: D 1034 LEU cc_start: 0.9321 (mp) cc_final: 0.8981 (tp) REVERT: D 1037 ASN cc_start: 0.9524 (m-40) cc_final: 0.9314 (m110) REVERT: D 1146 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8835 (mp0) outliers start: 53 outliers final: 22 residues processed: 285 average time/residue: 0.3570 time to fit residues: 170.4077 Evaluate side-chains 255 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 253 optimal weight: 5.9990 chunk 380 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 315 optimal weight: 50.0000 chunk 263 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 228 optimal weight: 0.6980 chunk 338 optimal weight: 0.8980 chunk 286 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.075009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.055759 restraints weight = 137960.973| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.87 r_work: 0.2718 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30396 Z= 0.138 Angle : 0.519 10.134 41392 Z= 0.262 Chirality : 0.036 0.157 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.957 87.447 4364 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.98 % Allowed : 10.52 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3848 helix: 2.52 (0.10), residues: 2512 sheet: -1.01 (0.37), residues: 244 loop : 0.21 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 680 HIS 0.007 0.001 HIS D 505 PHE 0.012 0.001 PHE A 627 TYR 0.008 0.001 TYR C1063 ARG 0.006 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 1936) hydrogen bonds : angle 4.43768 ( 5616) SS BOND : bond 0.00421 ( 4) SS BOND : angle 0.95208 ( 8) covalent geometry : bond 0.00304 (30392) covalent geometry : angle 0.51874 (41384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 3.326 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.9366 (tpp) cc_final: 0.8966 (mmm) REVERT: A 599 MET cc_start: 0.9061 (ttm) cc_final: 0.8845 (ttm) REVERT: A 622 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8852 (ttm) REVERT: A 930 VAL cc_start: 0.9159 (t) cc_final: 0.8895 (p) REVERT: A 1034 LEU cc_start: 0.9326 (mp) cc_final: 0.9019 (tp) REVERT: A 1037 ASN cc_start: 0.9528 (m-40) cc_final: 0.9315 (m110) REVERT: B 477 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9243 (mm) REVERT: B 599 MET cc_start: 0.9154 (ttm) cc_final: 0.8922 (ttm) REVERT: B 1034 LEU cc_start: 0.9217 (mp) cc_final: 0.8915 (tp) REVERT: B 1146 GLU cc_start: 0.9476 (mm-30) cc_final: 0.8978 (mp0) REVERT: C 477 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9258 (mm) REVERT: C 576 MET cc_start: 0.9220 (mmm) cc_final: 0.8857 (mmm) REVERT: C 580 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8909 (mt-10) REVERT: C 599 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8456 (ttp) REVERT: C 660 GLN cc_start: 0.9559 (OUTLIER) cc_final: 0.9091 (mt0) REVERT: C 951 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9315 (mp) REVERT: C 1034 LEU cc_start: 0.9237 (mp) cc_final: 0.8949 (tp) REVERT: C 1146 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9011 (mp0) REVERT: D 430 MET cc_start: 0.9624 (tpp) cc_final: 0.9284 (mmm) REVERT: D 477 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9249 (mm) REVERT: D 507 LEU cc_start: 0.9729 (mm) cc_final: 0.9462 (pp) REVERT: D 576 MET cc_start: 0.9265 (mmm) cc_final: 0.8929 (mmm) REVERT: D 580 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8920 (mt-10) REVERT: D 581 MET cc_start: 0.9447 (mmt) cc_final: 0.9224 (mtm) REVERT: D 599 MET cc_start: 0.9164 (ttm) cc_final: 0.8560 (ttp) REVERT: D 951 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9311 (mp) REVERT: D 1034 LEU cc_start: 0.9293 (mp) cc_final: 0.8956 (tp) outliers start: 57 outliers final: 26 residues processed: 298 average time/residue: 0.3507 time to fit residues: 177.1706 Evaluate side-chains 256 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 338 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 163 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 305 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 348 optimal weight: 0.0670 chunk 365 optimal weight: 9.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.075531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.056460 restraints weight = 137998.689| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.91 r_work: 0.2728 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30396 Z= 0.128 Angle : 0.527 10.527 41392 Z= 0.265 Chirality : 0.036 0.164 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.817 88.254 4362 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.86 % Allowed : 11.00 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.14), residues: 3848 helix: 2.55 (0.10), residues: 2512 sheet: -1.06 (0.36), residues: 244 loop : 0.18 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.007 0.001 HIS A 505 PHE 0.025 0.001 PHE C 373 TYR 0.008 0.001 TYR C1063 ARG 0.009 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 1936) hydrogen bonds : angle 4.37076 ( 5616) SS BOND : bond 0.00372 ( 4) SS BOND : angle 0.83295 ( 8) covalent geometry : bond 0.00282 (30392) covalent geometry : angle 0.52713 (41384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 3.544 Fit side-chains REVERT: A 136 ASP cc_start: 0.9718 (t0) cc_final: 0.9323 (m-30) REVERT: A 430 MET cc_start: 0.9399 (mmt) cc_final: 0.8946 (mmm) REVERT: A 576 MET cc_start: 0.9357 (tpp) cc_final: 0.8979 (mmm) REVERT: A 951 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9259 (mp) REVERT: A 1034 LEU cc_start: 0.9316 (mp) cc_final: 0.8999 (tp) REVERT: A 1037 ASN cc_start: 0.9528 (m-40) cc_final: 0.9285 (m110) REVERT: B 136 ASP cc_start: 0.9722 (t0) cc_final: 0.9319 (m-30) REVERT: B 430 MET cc_start: 0.9433 (mmt) cc_final: 0.9005 (mmm) REVERT: B 477 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9253 (mm) REVERT: B 602 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9549 (tt) REVERT: B 1034 LEU cc_start: 0.9207 (mp) cc_final: 0.8883 (tp) REVERT: B 1138 ARG cc_start: 0.9425 (ttp80) cc_final: 0.8905 (ttp80) REVERT: B 1146 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9003 (mp0) REVERT: C 136 ASP cc_start: 0.9727 (t0) cc_final: 0.9311 (m-30) REVERT: C 430 MET cc_start: 0.9499 (mmt) cc_final: 0.9023 (mmm) REVERT: C 477 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9249 (mm) REVERT: C 568 LEU cc_start: 0.9713 (mt) cc_final: 0.9507 (mt) REVERT: C 576 MET cc_start: 0.9246 (mmm) cc_final: 0.8916 (mmm) REVERT: C 580 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8940 (mt-10) REVERT: C 599 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8473 (ttp) REVERT: C 660 GLN cc_start: 0.9569 (OUTLIER) cc_final: 0.9120 (mt0) REVERT: C 951 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9317 (mp) REVERT: C 1034 LEU cc_start: 0.9175 (mp) cc_final: 0.8882 (tp) REVERT: C 1138 ARG cc_start: 0.9439 (ttp80) cc_final: 0.8926 (ttp80) REVERT: C 1146 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9034 (mp0) REVERT: D 136 ASP cc_start: 0.9737 (t0) cc_final: 0.9352 (m-30) REVERT: D 430 MET cc_start: 0.9632 (tpp) cc_final: 0.9230 (mmm) REVERT: D 477 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9246 (mm) REVERT: D 576 MET cc_start: 0.9298 (mmm) cc_final: 0.8970 (mmm) REVERT: D 580 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9004 (mt-10) REVERT: D 602 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9571 (tt) REVERT: D 951 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9328 (mp) REVERT: D 1034 LEU cc_start: 0.9258 (mp) cc_final: 0.8924 (tp) REVERT: D 1125 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8891 (tm-30) REVERT: D 1146 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9044 (mp0) outliers start: 82 outliers final: 32 residues processed: 318 average time/residue: 0.3433 time to fit residues: 187.2950 Evaluate side-chains 271 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 150 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 348 optimal weight: 0.0270 chunk 178 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 35 optimal weight: 0.0070 chunk 49 optimal weight: 10.0000 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.076507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057079 restraints weight = 139149.625| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.01 r_work: 0.2751 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30396 Z= 0.105 Angle : 0.527 11.764 41392 Z= 0.260 Chirality : 0.036 0.155 4788 Planarity : 0.004 0.049 5196 Dihedral : 6.691 88.262 4362 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 12.01 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3848 helix: 2.54 (0.10), residues: 2516 sheet: -1.07 (0.35), residues: 252 loop : 0.18 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.005 0.000 HIS C 505 PHE 0.018 0.001 PHE C 373 TYR 0.007 0.001 TYR B1063 ARG 0.008 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 1936) hydrogen bonds : angle 4.29419 ( 5616) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.71452 ( 8) covalent geometry : bond 0.00223 (30392) covalent geometry : angle 0.52661 (41384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 3.362 Fit side-chains REVERT: A 136 ASP cc_start: 0.9687 (t0) cc_final: 0.9335 (m-30) REVERT: A 576 MET cc_start: 0.9352 (tpp) cc_final: 0.9095 (mmm) REVERT: A 599 MET cc_start: 0.9096 (ttm) cc_final: 0.8851 (ttm) REVERT: A 675 LEU cc_start: 0.9548 (tp) cc_final: 0.9344 (tt) REVERT: A 951 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9271 (mp) REVERT: A 1034 LEU cc_start: 0.9304 (mp) cc_final: 0.8984 (tp) REVERT: B 175 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.9291 (mtp) REVERT: B 477 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9237 (mm) REVERT: B 509 MET cc_start: 0.9277 (ptm) cc_final: 0.9069 (mmt) REVERT: B 602 LEU cc_start: 0.9767 (OUTLIER) cc_final: 0.9546 (tt) REVERT: B 675 LEU cc_start: 0.9543 (tp) cc_final: 0.9322 (tt) REVERT: B 879 VAL cc_start: 0.9615 (t) cc_final: 0.9385 (m) REVERT: B 951 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9270 (mp) REVERT: B 1034 LEU cc_start: 0.9136 (mp) cc_final: 0.8840 (tp) REVERT: B 1146 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9071 (mp0) REVERT: C 136 ASP cc_start: 0.9697 (t0) cc_final: 0.9321 (m-30) REVERT: C 430 MET cc_start: 0.9542 (mmt) cc_final: 0.9245 (mmm) REVERT: C 477 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9241 (mm) REVERT: C 507 LEU cc_start: 0.9699 (mm) cc_final: 0.9458 (pp) REVERT: C 599 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8494 (ttp) REVERT: C 660 GLN cc_start: 0.9561 (OUTLIER) cc_final: 0.9113 (mt0) REVERT: C 879 VAL cc_start: 0.9599 (t) cc_final: 0.9387 (m) REVERT: C 922 ILE cc_start: 0.9378 (mt) cc_final: 0.9152 (mm) REVERT: C 951 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9311 (mp) REVERT: C 1034 LEU cc_start: 0.9198 (mp) cc_final: 0.8850 (tp) REVERT: C 1146 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9077 (mp0) REVERT: D 430 MET cc_start: 0.9674 (tpp) cc_final: 0.9318 (mmm) REVERT: D 477 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9248 (mm) REVERT: D 599 MET cc_start: 0.9168 (ttm) cc_final: 0.8695 (ttm) REVERT: D 602 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9570 (tt) REVERT: D 922 ILE cc_start: 0.9373 (mt) cc_final: 0.9162 (mm) REVERT: D 1034 LEU cc_start: 0.9262 (mp) cc_final: 0.8937 (tp) REVERT: D 1125 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8877 (tm-30) REVERT: D 1146 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9074 (mp0) outliers start: 57 outliers final: 25 residues processed: 326 average time/residue: 0.3536 time to fit residues: 194.9751 Evaluate side-chains 291 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 219 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 369 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 202 optimal weight: 30.0000 chunk 128 optimal weight: 40.0000 chunk 85 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.073840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054332 restraints weight = 141375.135| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.93 r_work: 0.2678 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 30396 Z= 0.305 Angle : 0.645 11.264 41392 Z= 0.322 Chirality : 0.039 0.173 4788 Planarity : 0.004 0.053 5196 Dihedral : 6.605 89.915 4362 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.47 % Allowed : 12.40 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.14), residues: 3848 helix: 2.59 (0.10), residues: 2464 sheet: -1.17 (0.35), residues: 252 loop : 0.12 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.008 0.001 HIS B1128 PHE 0.021 0.001 PHE B 373 TYR 0.010 0.001 TYR A 577 ARG 0.013 0.001 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1936) hydrogen bonds : angle 4.56094 ( 5616) SS BOND : bond 0.00683 ( 4) SS BOND : angle 0.63996 ( 8) covalent geometry : bond 0.00666 (30392) covalent geometry : angle 0.64538 (41384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 3.005 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.9392 (tpp) cc_final: 0.9119 (mmm) REVERT: A 581 MET cc_start: 0.9358 (mmm) cc_final: 0.9124 (mmm) REVERT: A 951 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9299 (mp) REVERT: A 1034 LEU cc_start: 0.9278 (mp) cc_final: 0.8933 (tp) REVERT: B 574 MET cc_start: 0.9391 (mpp) cc_final: 0.9150 (mmm) REVERT: B 951 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9275 (mp) REVERT: B 1034 LEU cc_start: 0.9233 (mp) cc_final: 0.8897 (tp) REVERT: B 1146 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9010 (mp0) REVERT: C 430 MET cc_start: 0.9538 (mmt) cc_final: 0.9196 (mmm) REVERT: C 477 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9256 (mm) REVERT: C 576 MET cc_start: 0.9483 (mmm) cc_final: 0.8752 (mmm) REVERT: C 580 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8731 (mp0) REVERT: C 599 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8709 (ttm) REVERT: C 660 GLN cc_start: 0.9621 (OUTLIER) cc_final: 0.9188 (mt0) REVERT: C 951 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9327 (mp) REVERT: C 1034 LEU cc_start: 0.9224 (mp) cc_final: 0.8870 (tp) REVERT: C 1146 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9029 (mp0) REVERT: D 576 MET cc_start: 0.9511 (mmm) cc_final: 0.8804 (mmm) REVERT: D 580 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8774 (mp0) REVERT: D 1034 LEU cc_start: 0.9308 (mp) cc_final: 0.8939 (tp) REVERT: D 1125 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9022 (tm-30) REVERT: D 1146 GLU cc_start: 0.9548 (mm-30) cc_final: 0.8967 (mp0) outliers start: 71 outliers final: 42 residues processed: 275 average time/residue: 0.3397 time to fit residues: 159.3562 Evaluate side-chains 259 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 249 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 341 optimal weight: 0.0870 chunk 182 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.075907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.056718 restraints weight = 138207.153| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.95 r_work: 0.2738 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30396 Z= 0.111 Angle : 0.561 12.577 41392 Z= 0.272 Chirality : 0.036 0.182 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.562 89.439 4360 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.88 % Allowed : 13.20 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.14), residues: 3848 helix: 2.54 (0.10), residues: 2488 sheet: -1.17 (0.35), residues: 252 loop : 0.08 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.008 0.001 HIS C 505 PHE 0.017 0.001 PHE B 373 TYR 0.008 0.001 TYR D 631 ARG 0.011 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 1936) hydrogen bonds : angle 4.34889 ( 5616) SS BOND : bond 0.00328 ( 4) SS BOND : angle 0.71289 ( 8) covalent geometry : bond 0.00240 (30392) covalent geometry : angle 0.56105 (41384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9368 (tpp) cc_final: 0.8981 (mmm) REVERT: A 580 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9128 (mt-10) REVERT: A 599 MET cc_start: 0.9118 (ttm) cc_final: 0.8848 (ttm) REVERT: A 951 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9291 (mp) REVERT: A 1034 LEU cc_start: 0.9265 (mp) cc_final: 0.8951 (tp) REVERT: B 136 ASP cc_start: 0.9713 (t0) cc_final: 0.9321 (m-30) REVERT: B 175 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.9241 (mtp) REVERT: B 509 MET cc_start: 0.9314 (ptm) cc_final: 0.9094 (mmt) REVERT: B 599 MET cc_start: 0.9087 (ttm) cc_final: 0.8817 (ttm) REVERT: B 602 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9537 (tt) REVERT: B 879 VAL cc_start: 0.9626 (t) cc_final: 0.9400 (m) REVERT: B 1034 LEU cc_start: 0.9150 (mp) cc_final: 0.8824 (tp) REVERT: B 1146 GLU cc_start: 0.9522 (mm-30) cc_final: 0.9055 (mp0) REVERT: C 136 ASP cc_start: 0.9721 (t0) cc_final: 0.9333 (m-30) REVERT: C 175 MET cc_start: 0.9561 (mtp) cc_final: 0.9295 (mtp) REVERT: C 315 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8380 (mm) REVERT: C 430 MET cc_start: 0.9516 (mmt) cc_final: 0.9211 (mmm) REVERT: C 477 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9236 (mm) REVERT: C 576 MET cc_start: 0.9463 (mmm) cc_final: 0.8802 (mmm) REVERT: C 580 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8705 (mp0) REVERT: C 599 MET cc_start: 0.9106 (ttm) cc_final: 0.8633 (ttm) REVERT: C 879 VAL cc_start: 0.9611 (t) cc_final: 0.9401 (m) REVERT: C 1034 LEU cc_start: 0.9204 (mp) cc_final: 0.8852 (tp) REVERT: D 430 MET cc_start: 0.9658 (tpp) cc_final: 0.9203 (mmm) REVERT: D 477 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9255 (mm) REVERT: D 576 MET cc_start: 0.9510 (mmm) cc_final: 0.9222 (mmm) REVERT: D 1034 LEU cc_start: 0.9288 (mp) cc_final: 0.8960 (tp) REVERT: D 1125 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8946 (tm-30) outliers start: 54 outliers final: 27 residues processed: 304 average time/residue: 0.3744 time to fit residues: 192.5952 Evaluate side-chains 281 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 105 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 chunk 384 optimal weight: 0.8980 chunk 303 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.056656 restraints weight = 138135.834| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.99 r_work: 0.2741 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30396 Z= 0.117 Angle : 0.558 11.333 41392 Z= 0.270 Chirality : 0.036 0.191 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.428 89.501 4360 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.57 % Allowed : 13.47 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.14), residues: 3848 helix: 2.54 (0.10), residues: 2492 sheet: -1.12 (0.35), residues: 252 loop : 0.07 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.006 0.001 HIS D 505 PHE 0.016 0.001 PHE B 373 TYR 0.008 0.001 TYR B1063 ARG 0.009 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 1936) hydrogen bonds : angle 4.28320 ( 5616) SS BOND : bond 0.00349 ( 4) SS BOND : angle 0.65163 ( 8) covalent geometry : bond 0.00258 (30392) covalent geometry : angle 0.55763 (41384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.9717 (t0) cc_final: 0.9338 (m-30) REVERT: A 599 MET cc_start: 0.9125 (ttm) cc_final: 0.8860 (ttm) REVERT: A 951 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9273 (mp) REVERT: A 1034 LEU cc_start: 0.9269 (mp) cc_final: 0.8912 (tp) REVERT: B 136 ASP cc_start: 0.9702 (t0) cc_final: 0.9311 (m-30) REVERT: B 477 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9247 (mm) REVERT: B 509 MET cc_start: 0.9309 (ptm) cc_final: 0.9093 (mmt) REVERT: B 599 MET cc_start: 0.9075 (ttm) cc_final: 0.8802 (ttm) REVERT: B 602 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9555 (tt) REVERT: B 879 VAL cc_start: 0.9603 (t) cc_final: 0.9379 (m) REVERT: B 1034 LEU cc_start: 0.9179 (mp) cc_final: 0.8832 (tp) REVERT: B 1146 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9124 (mp0) REVERT: C 175 MET cc_start: 0.9549 (OUTLIER) cc_final: 0.9316 (mtp) REVERT: C 315 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8371 (mm) REVERT: C 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9247 (mm) REVERT: C 599 MET cc_start: 0.9114 (ttm) cc_final: 0.8645 (ttm) REVERT: C 879 VAL cc_start: 0.9597 (t) cc_final: 0.9389 (m) REVERT: C 1034 LEU cc_start: 0.9204 (mp) cc_final: 0.8834 (tp) REVERT: D 599 MET cc_start: 0.9063 (ttm) cc_final: 0.8581 (ttm) REVERT: D 1034 LEU cc_start: 0.9279 (mp) cc_final: 0.8917 (tp) REVERT: D 1125 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8975 (tm-30) outliers start: 45 outliers final: 31 residues processed: 295 average time/residue: 0.3459 time to fit residues: 174.5339 Evaluate side-chains 288 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 14 optimal weight: 7.9990 chunk 267 optimal weight: 0.0270 chunk 125 optimal weight: 30.0000 chunk 334 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 352 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.074949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.055555 restraints weight = 140166.342| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.95 r_work: 0.2702 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30396 Z= 0.217 Angle : 0.613 10.943 41392 Z= 0.299 Chirality : 0.038 0.249 4788 Planarity : 0.004 0.073 5196 Dihedral : 6.351 89.908 4360 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.39 % Allowed : 14.03 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.14), residues: 3848 helix: 2.66 (0.10), residues: 2468 sheet: -1.16 (0.35), residues: 252 loop : 0.09 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1124 HIS 0.007 0.001 HIS C 505 PHE 0.013 0.001 PHE B 373 TYR 0.009 0.001 TYR C1063 ARG 0.017 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 1936) hydrogen bonds : angle 4.41412 ( 5616) SS BOND : bond 0.00592 ( 4) SS BOND : angle 0.62832 ( 8) covalent geometry : bond 0.00483 (30392) covalent geometry : angle 0.61335 (41384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 951 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9297 (mp) REVERT: A 1034 LEU cc_start: 0.9286 (mp) cc_final: 0.8903 (tp) REVERT: B 477 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9247 (mm) REVERT: B 509 MET cc_start: 0.9316 (ptm) cc_final: 0.9071 (mmt) REVERT: B 1034 LEU cc_start: 0.9234 (mp) cc_final: 0.8874 (tp) REVERT: B 1146 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9056 (mp0) REVERT: C 175 MET cc_start: 0.9580 (OUTLIER) cc_final: 0.9355 (mtp) REVERT: C 580 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8952 (mp0) REVERT: C 599 MET cc_start: 0.9075 (ttm) cc_final: 0.8789 (ttm) REVERT: C 879 VAL cc_start: 0.9633 (t) cc_final: 0.9431 (m) REVERT: C 1034 LEU cc_start: 0.9210 (mp) cc_final: 0.8825 (tp) REVERT: C 1146 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9065 (mp0) REVERT: D 430 MET cc_start: 0.9507 (mmt) cc_final: 0.9028 (mmm) REVERT: D 580 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8970 (mp0) REVERT: D 1034 LEU cc_start: 0.9182 (mp) cc_final: 0.8838 (tp) REVERT: D 1125 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9041 (tm-30) REVERT: D 1146 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9056 (mp0) outliers start: 40 outliers final: 33 residues processed: 276 average time/residue: 0.3596 time to fit residues: 168.5751 Evaluate side-chains 274 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 175 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 350 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 344 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.076560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057006 restraints weight = 139186.425| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.01 r_work: 0.2749 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30396 Z= 0.112 Angle : 0.578 12.484 41392 Z= 0.277 Chirality : 0.037 0.286 4788 Planarity : 0.004 0.055 5196 Dihedral : 6.269 88.201 4360 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.36 % Allowed : 14.17 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.14), residues: 3848 helix: 2.49 (0.10), residues: 2516 sheet: -1.14 (0.35), residues: 252 loop : 0.02 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 776 HIS 0.006 0.001 HIS D 505 PHE 0.015 0.001 PHE B 373 TYR 0.007 0.001 TYR D1063 ARG 0.013 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 1936) hydrogen bonds : angle 4.30699 ( 5616) SS BOND : bond 0.00324 ( 4) SS BOND : angle 0.67300 ( 8) covalent geometry : bond 0.00246 (30392) covalent geometry : angle 0.57803 (41384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13030.10 seconds wall clock time: 226 minutes 47.31 seconds (13607.31 seconds total)