Starting phenix.real_space_refine on Wed Jun 25 21:53:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b90_44364/06_2025/9b90_44364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b90_44364/06_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_44364/06_2025/9b90_44364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b90_44364/06_2025/9b90_44364.map" model { file = "/net/cci-nas-00/data/ceres_data/9b90_44364/06_2025/9b90_44364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b90_44364/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 20.36, per 1000 atoms: 0.69 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: 7.98 Conformation dependent library (CDL) restraints added in 3.6 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: 3.52 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: 13.78 Time building geometry restraints manager: 9.38 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: 0.23 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: 3.030 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: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 70.700 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.140 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.290 ------------------------------------------------------------------------------- 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 : 3.224 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: 0.4122 time to fit residues: 189.8967 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 : 3.201 ------------------------------------------------------------------------------- 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 = 0.074137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054755 restraints weight = 139882.967| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.87 r_work: 0.2689 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9370 (tpp) cc_final: 0.8943 (mmm) REVERT: A 669 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 930 VAL cc_start: 0.9276 (t) cc_final: 0.9003 (p) REVERT: A 1034 LEU cc_start: 0.9324 (mp) cc_final: 0.9028 (tp) REVERT: A 1037 ASN cc_start: 0.9536 (m-40) cc_final: 0.9317 (m110) REVERT: B 477 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9269 (mm) REVERT: B 576 MET cc_start: 0.9197 (mmm) cc_final: 0.8813 (mmm) REVERT: B 599 MET cc_start: 0.9125 (ttm) cc_final: 0.8921 (ttm) REVERT: B 669 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 951 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9294 (mp) REVERT: B 1034 LEU cc_start: 0.9277 (mp) cc_final: 0.8980 (tp) REVERT: B 1146 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8850 (mp0) REVERT: C 477 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9274 (mm) REVERT: C 576 MET cc_start: 0.9177 (mmm) cc_final: 0.8805 (mmm) REVERT: C 660 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.9078 (mt0) REVERT: C 669 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8242 (tm-30) REVERT: C 951 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9301 (mp) REVERT: C 1034 LEU cc_start: 0.9271 (mp) cc_final: 0.8995 (tp) REVERT: C 1146 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8804 (mp0) REVERT: D 175 MET cc_start: 0.9577 (OUTLIER) cc_final: 0.9297 (mtp) REVERT: D 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9256 (mm) REVERT: D 576 MET cc_start: 0.9238 (mmm) cc_final: 0.8664 (mmm) REVERT: D 669 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 951 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9322 (mp) REVERT: D 1034 LEU cc_start: 0.9324 (mp) cc_final: 0.8995 (tp) REVERT: D 1037 ASN cc_start: 0.9515 (m-40) cc_final: 0.9293 (m110) REVERT: D 1146 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8783 (mp0) outliers start: 48 outliers final: 14 residues processed: 281 average time/residue: 0.4041 time to fit residues: 187.1137 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 : 4.561 ------------------------------------------------------------------------------- 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: 9.9990 chunk 116 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 373 optimal weight: 0.9980 chunk 279 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 213 optimal weight: 0.0070 overall best weight: 2.7802 ------------------------------------------------------------------------------- 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 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 = 0.3535 r_free = 0.3535 target = 0.074569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055173 restraints weight = 138674.524| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.86 r_work: 0.2704 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30396 Z= 0.167 Angle : 0.544 9.466 41392 Z= 0.278 Chirality : 0.037 0.159 4788 Planarity : 0.004 0.046 5196 Dihedral : 7.148 86.385 4364 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.85 % Allowed : 9.33 % Favored : 88.82 % 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: 2.54 (0.10), residues: 2480 sheet: -1.03 (0.37), residues: 244 loop : 0.18 (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 0.006 0.000 ARG B1138 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 1936) hydrogen bonds : angle 4.65326 ( 5616) SS BOND : bond 0.00516 ( 4) SS BOND : angle 1.32717 ( 8) covalent geometry : bond 0.00369 (30392) covalent geometry : angle 0.54421 (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 300 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.9600 (tpp) cc_final: 0.9143 (mmm) REVERT: A 576 MET cc_start: 0.9407 (tpp) cc_final: 0.8914 (mmm) REVERT: A 580 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8963 (mt-10) REVERT: A 599 MET cc_start: 0.9151 (ttm) cc_final: 0.8772 (ttm) REVERT: A 930 VAL cc_start: 0.9205 (t) cc_final: 0.8948 (p) REVERT: A 951 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9251 (mp) REVERT: A 1034 LEU cc_start: 0.9325 (mp) cc_final: 0.9021 (tp) REVERT: A 1037 ASN cc_start: 0.9524 (m-40) cc_final: 0.9315 (m110) REVERT: A 1125 GLU cc_start: 0.9359 (tt0) cc_final: 0.9134 (tm-30) REVERT: B 477 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9247 (mm) REVERT: B 576 MET cc_start: 0.9234 (mmm) cc_final: 0.8756 (mmm) REVERT: B 599 MET cc_start: 0.9146 (ttm) cc_final: 0.8674 (ttm) REVERT: B 669 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8179 (tm-30) REVERT: B 951 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9325 (mp) REVERT: B 1034 LEU cc_start: 0.9210 (mp) cc_final: 0.8917 (tp) REVERT: B 1146 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8944 (mp0) REVERT: C 477 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9251 (mm) REVERT: C 576 MET cc_start: 0.9291 (mmm) cc_final: 0.8863 (mmm) REVERT: C 580 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8941 (mt-10) REVERT: C 599 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8575 (ttm) REVERT: C 660 GLN cc_start: 0.9532 (OUTLIER) cc_final: 0.9055 (mt0) REVERT: C 669 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 951 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9304 (mp) REVERT: C 1034 LEU cc_start: 0.9219 (mp) cc_final: 0.8948 (tp) REVERT: C 1125 GLU cc_start: 0.9394 (tt0) cc_final: 0.9146 (tt0) REVERT: C 1146 GLU cc_start: 0.9449 (mm-30) cc_final: 0.8874 (mp0) REVERT: D 430 MET cc_start: 0.9615 (tpp) cc_final: 0.9166 (mmm) REVERT: D 477 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9253 (mm) REVERT: D 576 MET cc_start: 0.9349 (mmm) cc_final: 0.8589 (mmm) REVERT: D 580 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8629 (mp0) REVERT: D 599 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8593 (ttm) REVERT: D 951 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9314 (mp) REVERT: D 1034 LEU cc_start: 0.9317 (mp) cc_final: 0.8973 (tp) REVERT: D 1037 ASN cc_start: 0.9521 (m-40) cc_final: 0.9313 (m110) REVERT: D 1146 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8834 (mp0) outliers start: 53 outliers final: 22 residues processed: 283 average time/residue: 0.3631 time to fit residues: 171.8161 Evaluate side-chains 249 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 3.119 ------------------------------------------------------------------------------- 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 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 599 MET 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: 0.9990 chunk 289 optimal weight: 9.9990 chunk 315 optimal weight: 50.0000 chunk 263 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 54 optimal weight: 0.0970 chunk 29 optimal weight: 20.0000 chunk 228 optimal weight: 0.6980 chunk 338 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.075477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.056327 restraints weight = 137306.360| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.84 r_work: 0.2734 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30396 Z= 0.112 Angle : 0.515 10.677 41392 Z= 0.259 Chirality : 0.036 0.157 4788 Planarity : 0.004 0.048 5196 Dihedral : 6.999 87.076 4364 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.92 % Allowed : 10.31 % Favored : 87.78 % 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: 2.50 (0.10), residues: 2512 sheet: -1.00 (0.37), residues: 244 loop : 0.22 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1058 HIS 0.008 0.001 HIS D 505 PHE 0.012 0.001 PHE D 627 TYR 0.008 0.001 TYR C1063 ARG 0.009 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 1936) hydrogen bonds : angle 4.42843 ( 5616) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.95123 ( 8) covalent geometry : bond 0.00240 (30392) covalent geometry : angle 0.51451 (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 316 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 3.436 Fit side-chains REVERT: A 507 LEU cc_start: 0.9711 (mm) cc_final: 0.9482 (pp) REVERT: A 576 MET cc_start: 0.9384 (tpp) cc_final: 0.9035 (mmm) REVERT: A 599 MET cc_start: 0.9129 (ttm) cc_final: 0.8754 (ttm) REVERT: A 1034 LEU cc_start: 0.9324 (mp) cc_final: 0.9021 (tp) REVERT: A 1037 ASN cc_start: 0.9521 (m-40) cc_final: 0.9299 (m110) REVERT: B 430 MET cc_start: 0.9624 (tpp) cc_final: 0.9023 (mmm) REVERT: B 477 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9238 (mm) REVERT: B 1034 LEU cc_start: 0.9211 (mp) cc_final: 0.8917 (tp) REVERT: B 1146 GLU cc_start: 0.9449 (mm-30) cc_final: 0.8970 (mp0) REVERT: C 477 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9242 (mm) REVERT: C 507 LEU cc_start: 0.9716 (mm) cc_final: 0.9434 (pp) REVERT: C 568 LEU cc_start: 0.9717 (mt) cc_final: 0.9504 (mt) REVERT: C 576 MET cc_start: 0.9251 (mmm) cc_final: 0.8896 (mmm) REVERT: C 580 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8908 (mt-10) REVERT: C 599 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8440 (ttp) REVERT: C 660 GLN cc_start: 0.9552 (OUTLIER) cc_final: 0.9084 (mt0) REVERT: C 951 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9292 (mp) REVERT: C 1034 LEU cc_start: 0.9221 (mp) cc_final: 0.8935 (tp) REVERT: C 1146 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9011 (mp0) REVERT: D 430 MET cc_start: 0.9623 (tpp) cc_final: 0.9277 (mmm) REVERT: D 477 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9249 (mm) REVERT: D 507 LEU cc_start: 0.9727 (mm) cc_final: 0.9481 (pp) REVERT: D 568 LEU cc_start: 0.9712 (mt) cc_final: 0.9467 (mt) REVERT: D 576 MET cc_start: 0.9403 (mmm) cc_final: 0.8982 (mmm) REVERT: D 580 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8903 (mt-10) REVERT: D 581 MET cc_start: 0.9428 (mmt) cc_final: 0.9209 (mpp) REVERT: D 599 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8416 (ttp) REVERT: D 951 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9305 (mp) REVERT: D 1034 LEU cc_start: 0.9291 (mp) cc_final: 0.8960 (tp) REVERT: D 1146 GLU cc_start: 0.9471 (mm-30) cc_final: 0.8889 (mp0) outliers start: 55 outliers final: 27 residues processed: 304 average time/residue: 0.3780 time to fit residues: 193.8504 Evaluate side-chains 264 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 3.149 ------------------------------------------------------------------------------- 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 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 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET 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: 20.0000 chunk 21 optimal weight: 50.0000 chunk 163 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 305 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 348 optimal weight: 0.0980 chunk 365 optimal weight: 10.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1037 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 = 0.3567 r_free = 0.3567 target = 0.076290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057217 restraints weight = 137200.281| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.97 r_work: 0.2755 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30396 Z= 0.105 Angle : 0.517 10.513 41392 Z= 0.258 Chirality : 0.036 0.177 4788 Planarity : 0.004 0.048 5196 Dihedral : 6.809 87.334 4362 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.51 % Allowed : 11.35 % 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: 2.44 (0.14), residues: 3848 helix: 2.51 (0.10), residues: 2512 sheet: -1.07 (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 B 772 HIS 0.005 0.001 HIS A 505 PHE 0.028 0.001 PHE C 373 TYR 0.007 0.001 TYR C1063 ARG 0.007 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 1936) hydrogen bonds : angle 4.30928 ( 5616) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.77957 ( 8) covalent geometry : bond 0.00219 (30392) covalent geometry : angle 0.51719 (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 353 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 281 time to evaluate : 3.545 Fit side-chains revert: symmetry clash REVERT: A 136 ASP cc_start: 0.9710 (t0) cc_final: 0.9302 (m-30) REVERT: A 507 LEU cc_start: 0.9724 (mm) cc_final: 0.9445 (pp) REVERT: A 576 MET cc_start: 0.9367 (tpp) cc_final: 0.9006 (mmm) REVERT: A 599 MET cc_start: 0.9157 (ttm) cc_final: 0.8731 (ttm) REVERT: A 622 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8802 (ttm) REVERT: A 951 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9257 (mp) REVERT: A 1034 LEU cc_start: 0.9318 (mp) cc_final: 0.9003 (tp) REVERT: B 136 ASP cc_start: 0.9711 (t0) cc_final: 0.9295 (m-30) REVERT: B 599 MET cc_start: 0.9173 (ttm) cc_final: 0.8751 (ttm) REVERT: B 602 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9563 (tt) REVERT: B 1034 LEU cc_start: 0.9198 (mp) cc_final: 0.8864 (tp) REVERT: B 1138 ARG cc_start: 0.9437 (ttp80) cc_final: 0.8918 (ttp80) REVERT: B 1146 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9025 (mp0) REVERT: C 136 ASP cc_start: 0.9718 (t0) cc_final: 0.9309 (m-30) REVERT: C 430 MET cc_start: 0.9470 (mmt) cc_final: 0.9027 (mmm) REVERT: C 477 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9233 (mm) REVERT: C 507 LEU cc_start: 0.9722 (mm) cc_final: 0.9415 (pp) REVERT: C 576 MET cc_start: 0.9256 (mmm) cc_final: 0.8946 (mmm) REVERT: C 580 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8972 (mt-10) REVERT: C 599 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8458 (ttp) REVERT: C 660 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9100 (mt0) REVERT: C 951 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9273 (mp) REVERT: C 1034 LEU cc_start: 0.9146 (mp) cc_final: 0.8852 (tp) REVERT: C 1138 ARG cc_start: 0.9457 (ttp80) cc_final: 0.8941 (ttp80) REVERT: C 1146 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9035 (mp0) REVERT: D 136 ASP cc_start: 0.9718 (t0) cc_final: 0.9361 (m-30) REVERT: D 430 MET cc_start: 0.9630 (tpp) cc_final: 0.9269 (mmm) REVERT: D 477 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9236 (mm) REVERT: D 507 LEU cc_start: 0.9714 (mm) cc_final: 0.9443 (pp) REVERT: D 568 LEU cc_start: 0.9691 (mt) cc_final: 0.9464 (mt) REVERT: D 576 MET cc_start: 0.9339 (mmm) cc_final: 0.9016 (mmm) REVERT: D 580 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8985 (mt-10) REVERT: D 599 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8432 (ttp) REVERT: D 922 ILE cc_start: 0.9378 (mt) cc_final: 0.9158 (mm) REVERT: D 1034 LEU cc_start: 0.9263 (mp) cc_final: 0.8945 (tp) REVERT: D 1037 ASN cc_start: 0.9480 (m-40) cc_final: 0.9212 (m110) outliers start: 72 outliers final: 25 residues processed: 339 average time/residue: 0.3657 time to fit residues: 211.8979 Evaluate side-chains 286 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 3.566 ------------------------------------------------------------------------------- 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 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 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 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 829 LEU Chi-restraints excluded: chain C residue 951 LEU 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 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 150 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 348 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.074946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.055562 restraints weight = 140935.131| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.95 r_work: 0.2700 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.005 0.052 30396 Z= 0.225 Angle : 0.589 11.360 41392 Z= 0.291 Chirality : 0.038 0.171 4788 Planarity : 0.004 0.052 5196 Dihedral : 6.639 88.508 4360 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.05 % Allowed : 12.08 % Favored : 85.86 % 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: 2.55 (0.14), residues: 3848 helix: 2.63 (0.10), residues: 2492 sheet: -1.05 (0.35), residues: 252 loop : 0.22 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.009 0.001 HIS A 505 PHE 0.019 0.001 PHE C 373 TYR 0.008 0.001 TYR C1063 ARG 0.012 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1936) hydrogen bonds : angle 4.43609 ( 5616) SS BOND : bond 0.00555 ( 4) SS BOND : angle 0.70186 ( 8) covalent geometry : bond 0.00498 (30392) covalent geometry : angle 0.58880 (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 298 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 3.245 Fit side-chains REVERT: A 136 ASP cc_start: 0.9709 (t0) cc_final: 0.9335 (m-30) REVERT: A 576 MET cc_start: 0.9374 (tpp) cc_final: 0.9110 (mmm) REVERT: A 951 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9280 (mp) REVERT: A 988 MET cc_start: 0.8982 (ptp) cc_final: 0.8774 (ptp) REVERT: A 1034 LEU cc_start: 0.9300 (mp) cc_final: 0.8971 (tp) REVERT: B 136 ASP cc_start: 0.9713 (t0) cc_final: 0.9367 (m-30) REVERT: B 477 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9263 (mm) REVERT: B 1034 LEU cc_start: 0.9205 (mp) cc_final: 0.8880 (tp) REVERT: B 1146 GLU cc_start: 0.9522 (mm-30) cc_final: 0.9030 (mp0) REVERT: C 136 ASP cc_start: 0.9720 (t0) cc_final: 0.9340 (m-30) REVERT: C 430 MET cc_start: 0.9568 (mmt) cc_final: 0.9230 (mmm) REVERT: C 477 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9245 (mm) REVERT: C 568 LEU cc_start: 0.9727 (mt) cc_final: 0.9479 (mt) REVERT: C 576 MET cc_start: 0.9333 (mmm) cc_final: 0.8905 (mmm) REVERT: C 580 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8859 (mt-10) REVERT: C 599 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8483 (ttp) REVERT: C 660 GLN cc_start: 0.9596 (OUTLIER) cc_final: 0.9155 (mt0) REVERT: C 951 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9337 (mp) REVERT: C 1034 LEU cc_start: 0.9216 (mp) cc_final: 0.8851 (tp) REVERT: C 1146 GLU cc_start: 0.9524 (mm-30) cc_final: 0.9036 (mp0) REVERT: D 430 MET cc_start: 0.9670 (tpp) cc_final: 0.9282 (mmm) REVERT: D 576 MET cc_start: 0.9372 (mmm) cc_final: 0.8963 (mmm) REVERT: D 580 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8927 (mt-10) REVERT: D 599 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8463 (ttp) REVERT: D 1034 LEU cc_start: 0.9301 (mp) cc_final: 0.8950 (tp) REVERT: D 1146 GLU cc_start: 0.9560 (mm-30) cc_final: 0.9055 (mp0) outliers start: 59 outliers final: 34 residues processed: 280 average time/residue: 0.3498 time to fit residues: 166.9561 Evaluate side-chains 269 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 3.228 ------------------------------------------------------------------------------- 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 622 MET Chi-restraints excluded: chain A residue 636 VAL 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 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 988 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 872 LEU 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 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 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET 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 1157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 219 optimal weight: 9.9990 chunk 358 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 369 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 202 optimal weight: 40.0000 chunk 128 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.074564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055110 restraints weight = 140541.637| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.92 r_work: 0.2690 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30396 Z= 0.221 Angle : 0.587 11.558 41392 Z= 0.292 Chirality : 0.038 0.194 4788 Planarity : 0.004 0.052 5196 Dihedral : 6.571 89.960 4358 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.47 % Allowed : 11.91 % Favored : 85.62 % 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: 2.47 (0.14), residues: 3848 helix: 2.62 (0.10), residues: 2464 sheet: -1.18 (0.35), residues: 252 loop : 0.13 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.007 0.001 HIS C 505 PHE 0.016 0.001 PHE C 373 TYR 0.009 0.001 TYR C1063 ARG 0.005 0.000 ARG D1138 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1936) hydrogen bonds : angle 4.46932 ( 5616) SS BOND : bond 0.00584 ( 4) SS BOND : angle 0.70559 ( 8) covalent geometry : bond 0.00488 (30392) covalent geometry : angle 0.58743 (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 302 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 231 time to evaluate : 3.609 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.9373 (tpp) cc_final: 0.9104 (mmm) REVERT: A 599 MET cc_start: 0.9139 (ttm) cc_final: 0.8750 (ttm) REVERT: A 951 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9281 (mp) REVERT: A 1034 LEU cc_start: 0.9293 (mp) cc_final: 0.8947 (tp) REVERT: B 477 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9300 (mm) REVERT: B 599 MET cc_start: 0.9171 (ttm) cc_final: 0.8793 (ttm) REVERT: B 951 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9285 (mp) REVERT: B 1034 LEU cc_start: 0.9219 (mp) cc_final: 0.8888 (tp) REVERT: B 1146 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9018 (mp0) REVERT: C 430 MET cc_start: 0.9568 (mmt) cc_final: 0.9218 (mmm) REVERT: C 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9266 (mm) REVERT: C 568 LEU cc_start: 0.9719 (mt) cc_final: 0.9517 (mt) REVERT: C 576 MET cc_start: 0.9321 (mmm) cc_final: 0.8923 (mmm) REVERT: C 580 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8933 (mt-10) REVERT: C 599 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8742 (ttm) REVERT: C 660 GLN cc_start: 0.9605 (OUTLIER) cc_final: 0.9168 (mt0) REVERT: C 951 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9316 (mp) REVERT: C 1034 LEU cc_start: 0.9207 (mp) cc_final: 0.8859 (tp) REVERT: C 1146 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9018 (mp0) REVERT: D 477 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9285 (mm) REVERT: D 576 MET cc_start: 0.9396 (mmm) cc_final: 0.9014 (mmm) REVERT: D 580 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9012 (mt-10) REVERT: D 599 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8781 (ttm) REVERT: D 1034 LEU cc_start: 0.9298 (mp) cc_final: 0.8956 (tp) REVERT: D 1146 GLU cc_start: 0.9547 (mm-30) cc_final: 0.8958 (mp0) outliers start: 71 outliers final: 37 residues processed: 282 average time/residue: 0.3625 time to fit residues: 174.1409 Evaluate side-chains 266 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 3.429 ------------------------------------------------------------------------------- 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 622 MET Chi-restraints excluded: chain A residue 636 VAL 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 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 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 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU 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 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 477 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET 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 900 MET Chi-restraints excluded: chain D residue 1032 ASN 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: 5.9990 chunk 380 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 382 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 341 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 263 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 chunk 150 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.076317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057193 restraints weight = 137608.749| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.99 r_work: 0.2748 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30396 Z= 0.108 Angle : 0.559 14.295 41392 Z= 0.271 Chirality : 0.037 0.207 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.520 89.055 4358 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.81 % Allowed : 13.09 % Favored : 85.10 % 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: 2.37 (0.14), residues: 3848 helix: 2.52 (0.10), residues: 2488 sheet: -1.15 (0.35), residues: 252 loop : 0.07 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 680 HIS 0.012 0.001 HIS A 505 PHE 0.015 0.001 PHE C 373 TYR 0.008 0.001 TYR D 631 ARG 0.009 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 1936) hydrogen bonds : angle 4.31917 ( 5616) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.68676 ( 8) covalent geometry : bond 0.00230 (30392) covalent geometry : angle 0.55941 (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 321 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.9710 (t0) cc_final: 0.9324 (m-30) REVERT: A 576 MET cc_start: 0.9387 (tpp) cc_final: 0.9101 (mmm) REVERT: A 599 MET cc_start: 0.9133 (ttm) cc_final: 0.8758 (ttm) REVERT: A 622 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8869 (ttm) REVERT: A 951 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9285 (mp) REVERT: A 1034 LEU cc_start: 0.9280 (mp) cc_final: 0.8966 (tp) REVERT: B 136 ASP cc_start: 0.9708 (t0) cc_final: 0.9306 (m-30) REVERT: B 477 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9234 (mm) REVERT: B 509 MET cc_start: 0.9313 (ptm) cc_final: 0.9080 (mmt) REVERT: B 599 MET cc_start: 0.9137 (ttm) cc_final: 0.8746 (ttm) REVERT: B 879 VAL cc_start: 0.9602 (t) cc_final: 0.9373 (m) REVERT: B 951 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9259 (mp) REVERT: B 1034 LEU cc_start: 0.9175 (mp) cc_final: 0.8834 (tp) REVERT: C 136 ASP cc_start: 0.9717 (t0) cc_final: 0.9324 (m-30) REVERT: C 430 MET cc_start: 0.9549 (mmt) cc_final: 0.9227 (mmm) REVERT: C 477 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 568 LEU cc_start: 0.9692 (mt) cc_final: 0.9485 (mt) REVERT: C 599 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8610 (ttm) REVERT: C 879 VAL cc_start: 0.9597 (t) cc_final: 0.9392 (m) REVERT: C 1034 LEU cc_start: 0.9178 (mp) cc_final: 0.8818 (tp) REVERT: D 136 ASP cc_start: 0.9718 (t0) cc_final: 0.9354 (m-30) REVERT: D 477 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9257 (mm) REVERT: D 509 MET cc_start: 0.9344 (ptm) cc_final: 0.9128 (mmt) REVERT: D 576 MET cc_start: 0.9397 (mmm) cc_final: 0.9032 (mmm) REVERT: D 580 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9027 (mt-10) REVERT: D 599 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8815 (ttm) REVERT: D 1034 LEU cc_start: 0.9285 (mp) cc_final: 0.8952 (tp) outliers start: 52 outliers final: 26 residues processed: 308 average time/residue: 0.3562 time to fit residues: 186.5843 Evaluate side-chains 288 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 3.598 ------------------------------------------------------------------------------- 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 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 876 LEU 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 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 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 175 MET 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 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 105 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 244 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 357 optimal weight: 2.9990 chunk 384 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.076021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.057025 restraints weight = 137337.707| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.92 r_work: 0.2740 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30396 Z= 0.129 Angle : 0.569 11.075 41392 Z= 0.276 Chirality : 0.037 0.199 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.411 89.079 4358 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.92 % Allowed : 13.09 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.37 (0.14), residues: 3848 helix: 2.51 (0.10), residues: 2492 sheet: -1.14 (0.35), residues: 252 loop : 0.09 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.016 0.001 HIS A 505 PHE 0.019 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 0.03324 ( 1936) hydrogen bonds : angle 4.31263 ( 5616) SS BOND : bond 0.00381 ( 4) SS BOND : angle 0.63964 ( 8) covalent geometry : bond 0.00289 (30392) covalent geometry : angle 0.56935 (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 318 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 6.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.9716 (t0) cc_final: 0.9332 (m-30) REVERT: A 576 MET cc_start: 0.9345 (tpp) cc_final: 0.8887 (mmm) REVERT: A 580 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9127 (mt-10) REVERT: A 599 MET cc_start: 0.9138 (ttm) cc_final: 0.8759 (ttm) REVERT: A 622 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8839 (ttm) REVERT: A 951 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9280 (mp) REVERT: A 1034 LEU cc_start: 0.9305 (mp) cc_final: 0.8949 (tp) REVERT: B 136 ASP cc_start: 0.9696 (t0) cc_final: 0.9300 (m-30) REVERT: B 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9246 (mm) REVERT: B 509 MET cc_start: 0.9311 (ptm) cc_final: 0.9070 (mmt) REVERT: B 879 VAL cc_start: 0.9602 (t) cc_final: 0.9379 (m) REVERT: B 951 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9276 (mp) REVERT: B 1034 LEU cc_start: 0.9197 (mp) cc_final: 0.8841 (tp) REVERT: B 1146 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9069 (mp0) REVERT: C 136 ASP cc_start: 0.9717 (t0) cc_final: 0.9314 (m-30) REVERT: C 315 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8394 (mm) REVERT: C 477 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9237 (mm) REVERT: C 568 LEU cc_start: 0.9690 (mt) cc_final: 0.9489 (mt) REVERT: C 580 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8894 (mp0) REVERT: C 599 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8785 (ttm) REVERT: C 879 VAL cc_start: 0.9598 (t) cc_final: 0.9394 (m) REVERT: C 1034 LEU cc_start: 0.9197 (mp) cc_final: 0.8833 (tp) REVERT: D 136 ASP cc_start: 0.9717 (t0) cc_final: 0.9361 (m-30) REVERT: D 430 MET cc_start: 0.9516 (mmt) cc_final: 0.9163 (mmm) REVERT: D 477 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9258 (mm) REVERT: D 509 MET cc_start: 0.9338 (ptm) cc_final: 0.9129 (mmt) REVERT: D 576 MET cc_start: 0.9433 (mmm) cc_final: 0.9057 (mmm) REVERT: D 580 GLU cc_start: 0.9270 (mt-10) cc_final: 0.9010 (mt-10) REVERT: D 599 MET cc_start: 0.9082 (ttm) cc_final: 0.8835 (ttm) REVERT: D 1034 LEU cc_start: 0.9283 (mp) cc_final: 0.8916 (tp) outliers start: 55 outliers final: 35 residues processed: 305 average time/residue: 0.5247 time to fit residues: 283.5839 Evaluate side-chains 297 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 3.400 ------------------------------------------------------------------------------- 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 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 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 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 599 MET 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 829 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 175 MET 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 574 MET Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 14 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 125 optimal weight: 30.0000 chunk 334 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 352 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.075473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056149 restraints weight = 139983.749| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.96 r_work: 0.2719 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30396 Z= 0.178 Angle : 0.598 12.027 41392 Z= 0.290 Chirality : 0.038 0.256 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.334 89.837 4358 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 13.58 % Favored : 84.68 % 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: 2.61 (0.10), residues: 2464 sheet: -1.14 (0.35), residues: 252 loop : 0.08 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.014 0.001 HIS A 505 PHE 0.014 0.001 PHE B 373 TYR 0.008 0.001 TYR C1063 ARG 0.008 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 1936) hydrogen bonds : angle 4.37149 ( 5616) SS BOND : bond 0.00496 ( 4) SS BOND : angle 0.63205 ( 8) covalent geometry : bond 0.00401 (30392) covalent geometry : angle 0.59833 (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 298 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9350 (tpp) cc_final: 0.9038 (mmm) REVERT: A 581 MET cc_start: 0.9352 (mmm) cc_final: 0.9122 (mmm) REVERT: A 951 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9291 (mp) REVERT: A 1034 LEU cc_start: 0.9317 (mp) cc_final: 0.8955 (tp) REVERT: B 136 ASP cc_start: 0.9713 (t0) cc_final: 0.9296 (m-30) REVERT: B 477 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9252 (mm) REVERT: B 509 MET cc_start: 0.9324 (ptm) cc_final: 0.9072 (mmt) REVERT: B 599 MET cc_start: 0.9144 (ttm) cc_final: 0.8794 (ttm) REVERT: B 879 VAL cc_start: 0.9622 (t) cc_final: 0.9409 (m) REVERT: B 951 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9279 (mp) REVERT: B 1034 LEU cc_start: 0.9225 (mp) cc_final: 0.8863 (tp) REVERT: B 1146 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9067 (mp0) REVERT: C 315 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8427 (mm) REVERT: C 477 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9249 (mm) REVERT: C 576 MET cc_start: 0.9483 (mmm) cc_final: 0.9142 (mmm) REVERT: C 580 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8943 (mp0) REVERT: C 599 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8762 (ttm) REVERT: C 879 VAL cc_start: 0.9620 (t) cc_final: 0.9420 (m) REVERT: C 1034 LEU cc_start: 0.9204 (mp) cc_final: 0.8830 (tp) REVERT: C 1146 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9077 (mp0) REVERT: D 477 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9277 (mm) REVERT: D 576 MET cc_start: 0.9403 (mmm) cc_final: 0.9015 (mmm) REVERT: D 580 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9024 (mt-10) REVERT: D 599 MET cc_start: 0.9078 (ttm) cc_final: 0.8808 (ttm) REVERT: D 1034 LEU cc_start: 0.9189 (mp) cc_final: 0.8846 (tp) REVERT: D 1146 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9084 (mp0) outliers start: 50 outliers final: 37 residues processed: 287 average time/residue: 0.4265 time to fit residues: 208.6640 Evaluate side-chains 289 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 3.868 ------------------------------------------------------------------------------- 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 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 951 LEU Chi-restraints excluded: chain B residue 1032 ASN 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 599 MET 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 829 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 175 MET 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 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET 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 876 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 175 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 350 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 308 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 344 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 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 = 0.3564 r_free = 0.3564 target = 0.076410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056875 restraints weight = 139349.295| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.00 r_work: 0.2744 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30396 Z= 0.118 Angle : 0.580 11.858 41392 Z= 0.279 Chirality : 0.037 0.272 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.243 88.464 4358 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.64 % Allowed : 13.82 % Favored : 84.54 % 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: 2.33 (0.14), residues: 3848 helix: 2.47 (0.10), residues: 2496 sheet: -1.13 (0.35), residues: 252 loop : 0.09 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1124 HIS 0.011 0.001 HIS A 505 PHE 0.015 0.001 PHE B 373 TYR 0.007 0.001 TYR D1063 ARG 0.007 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 1936) hydrogen bonds : angle 4.30908 ( 5616) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.66086 ( 8) covalent geometry : bond 0.00263 (30392) covalent geometry : angle 0.57961 (41384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14945.09 seconds wall clock time: 263 minutes 39.91 seconds (15819.91 seconds total)