Starting phenix.real_space_refine on Mon Aug 25 18:23:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b90_44364/08_2025/9b90_44364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b90_44364/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b90_44364/08_2025/9b90_44364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b90_44364/08_2025/9b90_44364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b90_44364/08_2025/9b90_44364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b90_44364/08_2025/9b90_44364.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 18, 'TRP:plan': 1, 'GLN:plan1': 5, 'ARG:plan': 17, 'ASP:plan': 19, 'HIS:plan': 3, 'PHE:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1} 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: B, C, D Time building chain proxies: 8.11, per 1000 atoms: 0.27 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 B 993 " - pdb=" SG CYS B1011 " distance=2.89 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.87 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: 6.16 Time building geometry restraints manager: 3.85 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.570 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG D 140 TYR 0.005 0.001 TYR B 968 PHE 0.006 0.001 PHE B1069 TRP 0.006 0.001 TRP C 776 HIS 0.002 0.001 HIS D1070 Details of bonding type rmsd covalent geometry : bond 0.00376 (30392) covalent geometry : angle 0.46791 (41384) SS BOND : bond 0.85409 ( 4) SS BOND : angle 21.29922 ( 8) hydrogen bonds : bond 0.19497 ( 1936) hydrogen bonds : angle 7.37161 ( 5616) *********************** 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 : 1.161 Fit side-chains 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 576 MET cc_start: 0.8698 (mmm) cc_final: 0.8470 (mmm) REVERT: C 1034 LEU cc_start: 0.9099 (mp) cc_final: 0.8819 (tp) REVERT: D 576 MET cc_start: 0.8725 (mmm) cc_final: 0.8516 (mmm) 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: 0.1835 time to fit residues: 84.6231 Evaluate side-chains 207 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 197 optimal weight: 20.0000 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN B 165 HIS B 410 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 GLN C 165 HIS C 410 GLN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 GLN D 410 GLN D 505 HIS D 973 GLN D1037 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.074497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055112 restraints weight = 139389.344| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.88 r_work: 0.2700 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30396 Z= 0.179 Angle : 0.591 10.813 41392 Z= 0.300 Chirality : 0.038 0.161 4788 Planarity : 0.004 0.041 5196 Dihedral : 7.557 86.134 4368 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.71 % Allowed : 7.63 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.14), residues: 3848 helix: 2.60 (0.10), residues: 2476 sheet: -1.01 (0.37), residues: 244 loop : 0.21 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 113 TYR 0.008 0.001 TYR D 227 PHE 0.018 0.001 PHE B 373 TRP 0.011 0.001 TRP A1058 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00394 (30392) covalent geometry : angle 0.59016 (41384) SS BOND : bond 0.00136 ( 4) SS BOND : angle 2.46246 ( 8) hydrogen bonds : bond 0.04545 ( 1936) hydrogen bonds : angle 4.85664 ( 5616) *********************** 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 303 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.9381 (tpp) cc_final: 0.8962 (mmm) REVERT: A 669 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 930 VAL cc_start: 0.9247 (t) cc_final: 0.8974 (p) REVERT: A 1034 LEU cc_start: 0.9329 (mp) cc_final: 0.9037 (tp) REVERT: A 1037 ASN cc_start: 0.9507 (m-40) cc_final: 0.9287 (m110) REVERT: B 477 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9264 (mm) REVERT: B 576 MET cc_start: 0.9253 (mmm) cc_final: 0.8906 (mmm) REVERT: B 580 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8907 (mt-10) REVERT: B 599 MET cc_start: 0.9127 (ttm) cc_final: 0.8913 (ttm) REVERT: B 669 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8307 (tm-30) REVERT: B 951 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9311 (mp) REVERT: B 1034 LEU cc_start: 0.9274 (mp) cc_final: 0.8982 (tp) REVERT: C 430 MET cc_start: 0.9670 (tpp) cc_final: 0.9258 (mmm) REVERT: C 477 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9270 (mm) REVERT: C 576 MET cc_start: 0.9422 (mmm) cc_final: 0.8624 (mmm) REVERT: C 580 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8623 (mp0) REVERT: C 660 GLN cc_start: 0.9525 (OUTLIER) cc_final: 0.9071 (mt0) REVERT: C 669 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 951 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9307 (mp) REVERT: C 1034 LEU cc_start: 0.9277 (mp) cc_final: 0.8996 (tp) REVERT: C 1146 GLU cc_start: 0.9394 (mm-30) cc_final: 0.8818 (mp0) REVERT: D 175 MET cc_start: 0.9575 (OUTLIER) cc_final: 0.9280 (mtp) REVERT: D 430 MET cc_start: 0.9645 (tpp) cc_final: 0.9226 (mmm) REVERT: D 477 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9254 (mm) REVERT: D 576 MET cc_start: 0.9413 (mmm) cc_final: 0.9037 (mmm) REVERT: D 580 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8962 (mt-10) REVERT: D 669 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 951 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9314 (mp) REVERT: D 1034 LEU cc_start: 0.9325 (mp) cc_final: 0.9008 (tp) REVERT: D 1130 GLU cc_start: 0.9530 (tt0) cc_final: 0.9315 (tt0) REVERT: D 1146 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8793 (mp0) outliers start: 49 outliers final: 14 residues processed: 289 average time/residue: 0.1930 time to fit residues: 92.3823 Evaluate side-chains 232 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 180 optimal weight: 20.0000 chunk 272 optimal weight: 0.8980 chunk 377 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 148 optimal weight: 7.9990 chunk 348 optimal weight: 0.0670 overall best weight: 2.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 410 GLN C 410 GLN C1061 GLN D 410 GLN D 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.074984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055712 restraints weight = 139047.575| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.89 r_work: 0.2718 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30396 Z= 0.149 Angle : 0.531 8.978 41392 Z= 0.271 Chirality : 0.037 0.159 4788 Planarity : 0.004 0.045 5196 Dihedral : 7.096 86.054 4364 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.92 % Allowed : 9.54 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.14), residues: 3848 helix: 2.57 (0.10), residues: 2480 sheet: -1.00 (0.37), residues: 244 loop : 0.16 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1138 TYR 0.007 0.001 TYR D 227 PHE 0.012 0.001 PHE B 373 TRP 0.009 0.001 TRP D 680 HIS 0.013 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00328 (30392) covalent geometry : angle 0.53055 (41384) SS BOND : bond 0.00337 ( 4) SS BOND : angle 1.25761 ( 8) hydrogen bonds : bond 0.03937 ( 1936) hydrogen bonds : angle 4.58173 ( 5616) *********************** 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 307 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 252 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9355 (tpp) cc_final: 0.8844 (mmm) REVERT: A 580 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8884 (mt-10) REVERT: A 599 MET cc_start: 0.9151 (ttm) cc_final: 0.8776 (ttm) REVERT: A 622 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8881 (ttm) REVERT: A 930 VAL cc_start: 0.9171 (t) cc_final: 0.8900 (p) REVERT: A 951 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9286 (mp) REVERT: A 1034 LEU cc_start: 0.9317 (mp) cc_final: 0.9015 (tp) REVERT: A 1037 ASN cc_start: 0.9533 (m-40) cc_final: 0.9321 (m110) REVERT: A 1125 GLU cc_start: 0.9358 (tt0) cc_final: 0.9149 (tm-30) REVERT: B 430 MET cc_start: 0.9611 (tpp) cc_final: 0.9036 (mmm) REVERT: B 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9251 (mm) REVERT: B 576 MET cc_start: 0.9192 (mmm) cc_final: 0.8771 (mmm) REVERT: B 599 MET cc_start: 0.9177 (ttm) cc_final: 0.8717 (ttm) REVERT: B 669 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 1034 LEU cc_start: 0.9197 (mp) cc_final: 0.8899 (tp) REVERT: C 477 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9242 (mm) REVERT: C 576 MET cc_start: 0.9406 (mmm) cc_final: 0.8874 (mmm) REVERT: C 580 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8913 (mt-10) REVERT: C 599 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8587 (ttm) REVERT: C 660 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.9056 (mt0) REVERT: C 669 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 951 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9312 (mp) REVERT: C 1034 LEU cc_start: 0.9228 (mp) cc_final: 0.8953 (tp) REVERT: C 1125 GLU cc_start: 0.9374 (tt0) cc_final: 0.9147 (tt0) REVERT: C 1146 GLU cc_start: 0.9468 (mm-30) cc_final: 0.8909 (mp0) REVERT: D 477 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9248 (mm) REVERT: D 576 MET cc_start: 0.9386 (mmm) cc_final: 0.8757 (mmm) REVERT: D 580 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8848 (mt-10) REVERT: D 622 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8888 (ttp) REVERT: D 951 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9326 (mp) REVERT: D 1034 LEU cc_start: 0.9286 (mp) cc_final: 0.8912 (tp) REVERT: D 1146 GLU cc_start: 0.9433 (mm-30) cc_final: 0.8842 (mp0) outliers start: 55 outliers final: 21 residues processed: 291 average time/residue: 0.1840 time to fit residues: 89.7136 Evaluate side-chains 252 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 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 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 622 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 113 optimal weight: 20.0000 chunk 198 optimal weight: 30.0000 chunk 386 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 380 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.074047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.054637 restraints weight = 138713.198| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.89 r_work: 0.2690 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30396 Z= 0.226 Angle : 0.564 9.857 41392 Z= 0.285 Chirality : 0.037 0.158 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.945 87.897 4362 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.05 % Allowed : 10.55 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.14), residues: 3848 helix: 2.55 (0.10), residues: 2488 sheet: -1.02 (0.36), residues: 244 loop : 0.18 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 334 TYR 0.008 0.001 TYR D1063 PHE 0.024 0.001 PHE C 373 TRP 0.010 0.001 TRP A1124 HIS 0.009 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00501 (30392) covalent geometry : angle 0.56433 (41384) SS BOND : bond 0.00578 ( 4) SS BOND : angle 0.97461 ( 8) hydrogen bonds : bond 0.03817 ( 1936) hydrogen bonds : angle 4.56262 ( 5616) *********************** 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 277 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 1.256 Fit side-chains REVERT: A 576 MET cc_start: 0.9339 (tpp) cc_final: 0.8832 (mmm) REVERT: A 580 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8951 (mt-10) REVERT: A 599 MET cc_start: 0.9138 (ttm) cc_final: 0.8710 (ttm) REVERT: A 622 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8900 (ttm) REVERT: A 669 GLN cc_start: 0.8553 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 930 VAL cc_start: 0.9210 (t) cc_final: 0.8943 (p) REVERT: A 1034 LEU cc_start: 0.9329 (mp) cc_final: 0.9005 (tp) REVERT: A 1037 ASN cc_start: 0.9570 (m-40) cc_final: 0.9353 (m110) REVERT: B 477 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9249 (mm) REVERT: B 599 MET cc_start: 0.9156 (ttm) cc_final: 0.8869 (ttm) REVERT: B 669 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 1034 LEU cc_start: 0.9226 (mp) cc_final: 0.8922 (tp) REVERT: C 477 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9260 (mm) REVERT: C 576 MET cc_start: 0.9455 (mmm) cc_final: 0.8985 (mmm) REVERT: C 580 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8861 (mt-10) REVERT: C 599 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: C 660 GLN cc_start: 0.9570 (OUTLIER) cc_final: 0.9074 (mt0) REVERT: C 669 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 951 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9305 (mp) REVERT: C 1034 LEU cc_start: 0.9252 (mp) cc_final: 0.8965 (tp) REVERT: C 1125 GLU cc_start: 0.9395 (tt0) cc_final: 0.9174 (tt0) REVERT: C 1146 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9002 (mp0) REVERT: D 477 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9267 (mm) REVERT: D 576 MET cc_start: 0.9373 (mmm) cc_final: 0.8842 (mmm) REVERT: D 580 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8851 (mt-10) REVERT: D 669 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8315 (tm-30) REVERT: D 951 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9334 (mp) REVERT: D 1034 LEU cc_start: 0.9304 (mp) cc_final: 0.8927 (tp) REVERT: D 1146 GLU cc_start: 0.9501 (mm-30) cc_final: 0.8979 (mp0) outliers start: 59 outliers final: 30 residues processed: 263 average time/residue: 0.1812 time to fit residues: 81.1718 Evaluate side-chains 244 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 876 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 636 VAL Chi-restraints excluded: chain B residue 798 SER 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 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 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 244 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 348 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 361 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.076089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056989 restraints weight = 138758.462| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.91 r_work: 0.2742 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30396 Z= 0.107 Angle : 0.522 10.743 41392 Z= 0.260 Chirality : 0.036 0.157 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.828 88.661 4360 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 11.28 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.14), residues: 3848 helix: 2.56 (0.10), residues: 2488 sheet: -1.09 (0.36), residues: 244 loop : 0.12 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 113 TYR 0.008 0.001 TYR A 227 PHE 0.018 0.001 PHE C 373 TRP 0.009 0.001 TRP D 680 HIS 0.002 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00226 (30392) covalent geometry : angle 0.52168 (41384) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.85005 ( 8) hydrogen bonds : bond 0.03419 ( 1936) hydrogen bonds : angle 4.35542 ( 5616) *********************** 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 336 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 1.348 Fit side-chains REVERT: A 136 ASP cc_start: 0.9721 (t0) cc_final: 0.9309 (m-30) REVERT: A 576 MET cc_start: 0.9332 (tpp) cc_final: 0.8815 (mmm) REVERT: A 580 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8969 (mt-10) REVERT: A 622 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8827 (ttm) REVERT: A 951 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9258 (mp) REVERT: A 1034 LEU cc_start: 0.9308 (mp) cc_final: 0.8988 (tp) REVERT: A 1037 ASN cc_start: 0.9515 (m-40) cc_final: 0.9266 (m110) REVERT: B 136 ASP cc_start: 0.9734 (t0) cc_final: 0.9315 (m-30) REVERT: B 430 MET cc_start: 0.9401 (mmt) cc_final: 0.8965 (mmm) REVERT: B 477 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9251 (mm) REVERT: B 599 MET cc_start: 0.9195 (ttm) cc_final: 0.8980 (ttm) REVERT: B 602 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9541 (tt) REVERT: B 951 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9274 (mp) REVERT: B 1034 LEU cc_start: 0.9197 (mp) cc_final: 0.8889 (tp) REVERT: B 1138 ARG cc_start: 0.9437 (ttp80) cc_final: 0.8928 (ttp80) REVERT: C 136 ASP cc_start: 0.9720 (t0) cc_final: 0.9311 (m-30) REVERT: C 430 MET cc_start: 0.9575 (mmt) cc_final: 0.9023 (mmm) REVERT: C 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9228 (mm) REVERT: C 507 LEU cc_start: 0.9721 (mm) cc_final: 0.9449 (pp) REVERT: C 580 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9046 (mt-10) REVERT: C 599 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8819 (ttm) REVERT: C 602 LEU cc_start: 0.9786 (OUTLIER) cc_final: 0.9585 (tt) REVERT: C 660 GLN cc_start: 0.9564 (OUTLIER) cc_final: 0.9124 (mt0) REVERT: C 922 ILE cc_start: 0.9369 (mt) cc_final: 0.9109 (mm) REVERT: C 951 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9271 (mp) REVERT: C 1034 LEU cc_start: 0.9222 (mp) cc_final: 0.8914 (tp) REVERT: C 1146 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9033 (mp0) REVERT: D 136 ASP cc_start: 0.9725 (t0) cc_final: 0.9367 (m-30) REVERT: D 477 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9242 (mm) REVERT: D 507 LEU cc_start: 0.9715 (mm) cc_final: 0.9467 (pp) REVERT: D 580 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9038 (mt-10) REVERT: D 599 MET cc_start: 0.9142 (ttm) cc_final: 0.8844 (ttm) REVERT: D 602 LEU cc_start: 0.9778 (OUTLIER) cc_final: 0.9574 (tt) REVERT: D 1034 LEU cc_start: 0.9252 (mp) cc_final: 0.8927 (tp) REVERT: D 1125 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8849 (tm-30) REVERT: D 1146 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9038 (mp0) outliers start: 64 outliers final: 23 residues processed: 329 average time/residue: 0.1758 time to fit residues: 98.7683 Evaluate side-chains 280 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 602 LEU 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 1032 ASN 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 602 LEU 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 Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055276 restraints weight = 140515.253| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.92 r_work: 0.2696 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30396 Z= 0.226 Angle : 0.583 10.913 41392 Z= 0.290 Chirality : 0.038 0.196 4788 Planarity : 0.004 0.053 5196 Dihedral : 6.711 89.599 4360 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 12.01 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.14), residues: 3848 helix: 2.59 (0.10), residues: 2468 sheet: -1.10 (0.35), residues: 252 loop : 0.13 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 113 TYR 0.008 0.001 TYR C1063 PHE 0.020 0.001 PHE D 373 TRP 0.011 0.001 TRP B1124 HIS 0.010 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00501 (30392) covalent geometry : angle 0.58310 (41384) SS BOND : bond 0.00556 ( 4) SS BOND : angle 0.72708 ( 8) hydrogen bonds : bond 0.03638 ( 1936) hydrogen bonds : angle 4.46452 ( 5616) *********************** 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 299 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 1.184 Fit side-chains REVERT: A 576 MET cc_start: 0.9370 (tpp) cc_final: 0.8925 (mmm) REVERT: A 580 GLU cc_start: 0.9228 (mt-10) cc_final: 0.9003 (mt-10) REVERT: A 599 MET cc_start: 0.9135 (ttm) cc_final: 0.8751 (ttm) REVERT: A 951 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9291 (mp) REVERT: A 988 MET cc_start: 0.8952 (ptp) cc_final: 0.8742 (ptp) REVERT: A 1034 LEU cc_start: 0.9321 (mp) cc_final: 0.8986 (tp) REVERT: A 1037 ASN cc_start: 0.9543 (m-40) cc_final: 0.9283 (m110) REVERT: B 430 MET cc_start: 0.9439 (mmt) cc_final: 0.9077 (mmm) REVERT: B 951 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9287 (mp) REVERT: B 1034 LEU cc_start: 0.9239 (mp) cc_final: 0.8891 (tp) REVERT: C 580 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9038 (mt-10) REVERT: C 599 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8736 (ttm) REVERT: C 660 GLN cc_start: 0.9596 (OUTLIER) cc_final: 0.9151 (mt0) REVERT: C 951 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9330 (mp) REVERT: C 1034 LEU cc_start: 0.9176 (mp) cc_final: 0.8883 (tp) REVERT: C 1146 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9029 (mp0) REVERT: D 580 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9086 (mt-10) REVERT: D 1034 LEU cc_start: 0.9301 (mp) cc_final: 0.8951 (tp) REVERT: D 1146 GLU cc_start: 0.9543 (mm-30) cc_final: 0.8964 (mp0) outliers start: 62 outliers final: 32 residues processed: 279 average time/residue: 0.1752 time to fit residues: 83.9598 Evaluate side-chains 263 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL 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 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 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU 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 210 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 371 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 255 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.075483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056132 restraints weight = 138946.828| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.95 r_work: 0.2719 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30396 Z= 0.148 Angle : 0.551 11.558 41392 Z= 0.273 Chirality : 0.037 0.159 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.653 89.994 4360 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.05 % Allowed : 12.26 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.14), residues: 3848 helix: 2.61 (0.10), residues: 2468 sheet: -1.19 (0.35), residues: 252 loop : 0.09 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1138 TYR 0.008 0.001 TYR C1063 PHE 0.017 0.001 PHE D 373 TRP 0.009 0.001 TRP C 680 HIS 0.004 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00330 (30392) covalent geometry : angle 0.55079 (41384) SS BOND : bond 0.00441 ( 4) SS BOND : angle 0.74459 ( 8) hydrogen bonds : bond 0.03450 ( 1936) hydrogen bonds : angle 4.38495 ( 5616) *********************** 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 307 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 1.271 Fit side-chains REVERT: A 576 MET cc_start: 0.9374 (tpp) cc_final: 0.8985 (mmm) REVERT: A 580 GLU cc_start: 0.9250 (mt-10) cc_final: 0.9024 (mt-10) REVERT: A 951 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9279 (mp) REVERT: A 988 MET cc_start: 0.8997 (ptp) cc_final: 0.8752 (ptp) REVERT: A 1034 LEU cc_start: 0.9322 (mp) cc_final: 0.8990 (tp) REVERT: A 1037 ASN cc_start: 0.9521 (m-40) cc_final: 0.9274 (m110) REVERT: B 136 ASP cc_start: 0.9742 (t0) cc_final: 0.9339 (m-30) REVERT: B 477 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9252 (mm) REVERT: B 602 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9527 (tt) REVERT: B 951 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9260 (mp) REVERT: B 1034 LEU cc_start: 0.9164 (mp) cc_final: 0.8858 (tp) REVERT: C 136 ASP cc_start: 0.9728 (t0) cc_final: 0.9360 (m-30) REVERT: C 477 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9242 (mm) REVERT: C 599 MET cc_start: 0.9124 (ttm) cc_final: 0.8589 (ttm) REVERT: C 660 GLN cc_start: 0.9591 (OUTLIER) cc_final: 0.9161 (mt0) REVERT: C 951 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9285 (mp) REVERT: C 1034 LEU cc_start: 0.9214 (mp) cc_final: 0.8879 (tp) REVERT: C 1146 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9028 (mp0) REVERT: D 136 ASP cc_start: 0.9730 (t0) cc_final: 0.9353 (m-30) REVERT: D 477 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9276 (mm) REVERT: D 580 GLU cc_start: 0.9292 (mt-10) cc_final: 0.9076 (mt-10) REVERT: D 1034 LEU cc_start: 0.9297 (mp) cc_final: 0.8956 (tp) REVERT: D 1125 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8947 (tm-30) REVERT: D 1146 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9035 (mp0) outliers start: 59 outliers final: 29 residues processed: 294 average time/residue: 0.1768 time to fit residues: 88.2841 Evaluate side-chains 272 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 477 LEU 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 1125 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 307 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 360 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 319 optimal weight: 0.0970 chunk 373 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 200 optimal weight: 50.0000 chunk 278 optimal weight: 6.9990 overall best weight: 4.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.074412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054911 restraints weight = 141011.769| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.95 r_work: 0.2687 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30396 Z= 0.235 Angle : 0.611 11.560 41392 Z= 0.300 Chirality : 0.038 0.255 4788 Planarity : 0.004 0.052 5196 Dihedral : 6.569 89.339 4360 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.12 % Allowed : 12.92 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.14), residues: 3848 helix: 2.57 (0.10), residues: 2464 sheet: -1.22 (0.35), residues: 252 loop : 0.08 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 113 TYR 0.010 0.001 TYR C1063 PHE 0.015 0.001 PHE D 373 TRP 0.010 0.001 TRP B1124 HIS 0.010 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00519 (30392) covalent geometry : angle 0.61076 (41384) SS BOND : bond 0.00615 ( 4) SS BOND : angle 0.67917 ( 8) hydrogen bonds : bond 0.03685 ( 1936) hydrogen bonds : angle 4.50272 ( 5616) *********************** 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 290 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 229 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9366 (tpp) cc_final: 0.9007 (mmm) REVERT: A 581 MET cc_start: 0.9355 (mmm) cc_final: 0.9123 (mmm) REVERT: A 599 MET cc_start: 0.9141 (ttm) cc_final: 0.8741 (ttm) REVERT: A 951 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9283 (mp) REVERT: A 1034 LEU cc_start: 0.9314 (mp) cc_final: 0.8943 (tp) REVERT: A 1037 ASN cc_start: 0.9525 (m-40) cc_final: 0.9285 (m110) REVERT: B 477 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9262 (mm) REVERT: B 951 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9274 (mp) REVERT: B 1034 LEU cc_start: 0.9218 (mp) cc_final: 0.8869 (tp) REVERT: C 477 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9281 (mm) REVERT: C 580 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8894 (mp0) REVERT: C 599 MET cc_start: 0.9090 (ttm) cc_final: 0.8784 (ttm) REVERT: C 660 GLN cc_start: 0.9617 (OUTLIER) cc_final: 0.9188 (mt0) REVERT: C 951 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9320 (mp) REVERT: C 1034 LEU cc_start: 0.9219 (mp) cc_final: 0.8906 (tp) REVERT: C 1146 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9063 (mp0) REVERT: D 477 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9283 (mm) REVERT: D 580 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9089 (mt-10) REVERT: D 1034 LEU cc_start: 0.9231 (mp) cc_final: 0.8882 (tp) REVERT: D 1125 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.9018 (tm-30) REVERT: D 1146 GLU cc_start: 0.9548 (mm-30) cc_final: 0.8960 (mp0) outliers start: 61 outliers final: 31 residues processed: 273 average time/residue: 0.1771 time to fit residues: 83.0463 Evaluate side-chains 262 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 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 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 900 MET Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 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 1125 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 158 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.075903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056634 restraints weight = 138383.402| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.95 r_work: 0.2736 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30396 Z= 0.118 Angle : 0.571 11.269 41392 Z= 0.276 Chirality : 0.037 0.188 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.538 89.767 4360 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.36 % Allowed : 13.68 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.14), residues: 3848 helix: 2.50 (0.10), residues: 2492 sheet: -1.23 (0.35), residues: 252 loop : 0.04 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 113 TYR 0.007 0.001 TYR A1063 PHE 0.016 0.001 PHE D 373 TRP 0.010 0.001 TRP D 680 HIS 0.004 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00258 (30392) covalent geometry : angle 0.57056 (41384) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.70236 ( 8) hydrogen bonds : bond 0.03349 ( 1936) hydrogen bonds : angle 4.37082 ( 5616) *********************** 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 297 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9376 (tpp) cc_final: 0.8984 (mmm) REVERT: A 580 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8996 (mt-10) REVERT: A 599 MET cc_start: 0.9141 (ttm) cc_final: 0.8791 (ttm) REVERT: A 951 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9293 (mp) REVERT: A 1034 LEU cc_start: 0.9314 (mp) cc_final: 0.8968 (tp) REVERT: B 175 MET cc_start: 0.9558 (OUTLIER) cc_final: 0.9249 (mtp) REVERT: B 477 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9238 (mm) REVERT: B 599 MET cc_start: 0.9077 (ttm) cc_final: 0.8857 (ttm) REVERT: B 879 VAL cc_start: 0.9619 (t) cc_final: 0.9394 (m) REVERT: B 951 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9258 (mp) REVERT: B 1034 LEU cc_start: 0.9207 (mp) cc_final: 0.8857 (tp) REVERT: C 136 ASP cc_start: 0.9729 (t0) cc_final: 0.9331 (m-30) REVERT: C 477 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9238 (mm) REVERT: C 580 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8933 (mp0) REVERT: C 599 MET cc_start: 0.9127 (ttm) cc_final: 0.8653 (ttm) REVERT: C 1034 LEU cc_start: 0.9222 (mp) cc_final: 0.8895 (tp) REVERT: D 136 ASP cc_start: 0.9735 (t0) cc_final: 0.9350 (m-30) REVERT: D 477 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9259 (mm) REVERT: D 509 MET cc_start: 0.9356 (ptm) cc_final: 0.9147 (mmt) REVERT: D 576 MET cc_start: 0.9434 (mmm) cc_final: 0.9201 (mmm) REVERT: D 1034 LEU cc_start: 0.9196 (mp) cc_final: 0.8853 (tp) REVERT: D 1125 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8982 (tm-30) outliers start: 39 outliers final: 26 residues processed: 289 average time/residue: 0.1841 time to fit residues: 90.8117 Evaluate side-chains 272 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 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 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 313 optimal weight: 20.0000 chunk 237 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 chunk 123 optimal weight: 0.0870 chunk 172 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 213 optimal weight: 0.0030 chunk 60 optimal weight: 4.9990 chunk 328 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1037 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 = 0.3544 r_free = 0.3544 target = 0.075306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056021 restraints weight = 138870.038| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.94 r_work: 0.2717 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2567 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= 0.169 Angle : 0.593 11.525 41392 Z= 0.288 Chirality : 0.037 0.240 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.440 89.952 4360 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.36 % Allowed : 14.14 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.14), residues: 3848 helix: 2.57 (0.10), residues: 2468 sheet: -1.21 (0.35), residues: 252 loop : 0.06 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 113 TYR 0.009 0.001 TYR C1063 PHE 0.013 0.001 PHE D 373 TRP 0.009 0.001 TRP B1124 HIS 0.004 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00378 (30392) covalent geometry : angle 0.59255 (41384) SS BOND : bond 0.00485 ( 4) SS BOND : angle 0.65470 ( 8) hydrogen bonds : bond 0.03474 ( 1936) hydrogen bonds : angle 4.41022 ( 5616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9324 (tpp) cc_final: 0.8886 (mmm) REVERT: A 580 GLU cc_start: 0.9243 (mt-10) cc_final: 0.9003 (mt-10) REVERT: A 581 MET cc_start: 0.9369 (mmm) cc_final: 0.9139 (mmm) REVERT: A 599 MET cc_start: 0.9139 (ttm) cc_final: 0.8775 (ttm) REVERT: A 951 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9297 (mp) REVERT: A 1034 LEU cc_start: 0.9282 (mp) cc_final: 0.8937 (tp) REVERT: B 136 ASP cc_start: 0.9744 (t0) cc_final: 0.9334 (m-30) REVERT: B 175 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9264 (mtp) REVERT: B 477 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9251 (mm) REVERT: B 599 MET cc_start: 0.9099 (ttm) cc_final: 0.8853 (ttm) REVERT: B 879 VAL cc_start: 0.9630 (t) cc_final: 0.9419 (m) REVERT: B 951 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9266 (mp) REVERT: B 1034 LEU cc_start: 0.9212 (mp) cc_final: 0.8854 (tp) REVERT: C 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9250 (mm) REVERT: C 576 MET cc_start: 0.9467 (mmm) cc_final: 0.9133 (mmm) REVERT: C 580 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8983 (mp0) REVERT: C 599 MET cc_start: 0.9097 (ttm) cc_final: 0.8809 (ttm) REVERT: C 1034 LEU cc_start: 0.9242 (mp) cc_final: 0.8914 (tp) REVERT: C 1146 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9074 (mp0) REVERT: D 477 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9277 (mm) REVERT: D 576 MET cc_start: 0.9514 (mmm) cc_final: 0.9111 (mmm) REVERT: D 580 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8982 (mp0) REVERT: D 1034 LEU cc_start: 0.9223 (mp) cc_final: 0.8850 (tp) REVERT: D 1125 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9024 (tm-30) REVERT: D 1146 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9032 (mp0) outliers start: 39 outliers final: 29 residues processed: 273 average time/residue: 0.1789 time to fit residues: 82.8791 Evaluate side-chains 277 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 276 LEU 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 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 477 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 104 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 chunk 201 optimal weight: 40.0000 chunk 281 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 384 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1037 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 = 0.3551 r_free = 0.3551 target = 0.075727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.056445 restraints weight = 139194.433| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.95 r_work: 0.2728 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30396 Z= 0.150 Angle : 0.581 11.268 41392 Z= 0.282 Chirality : 0.037 0.271 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.342 88.619 4360 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.39 % Allowed : 14.14 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.14), residues: 3848 helix: 2.56 (0.10), residues: 2472 sheet: -1.19 (0.35), residues: 252 loop : 0.05 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 113 TYR 0.008 0.001 TYR B 704 PHE 0.014 0.001 PHE D 373 TRP 0.009 0.001 TRP B1124 HIS 0.013 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00338 (30392) covalent geometry : angle 0.58108 (41384) SS BOND : bond 0.00445 ( 4) SS BOND : angle 0.68530 ( 8) hydrogen bonds : bond 0.03380 ( 1936) hydrogen bonds : angle 4.37646 ( 5616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7023.49 seconds wall clock time: 121 minutes 29.37 seconds (7289.37 seconds total)