Starting phenix.real_space_refine on Thu Jan 15 09:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd7_37127/01_2026/8kd7_37127.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd7_37127/01_2026/8kd7_37127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd7_37127/01_2026/8kd7_37127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd7_37127/01_2026/8kd7_37127.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd7_37127/01_2026/8kd7_37127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd7_37127/01_2026/8kd7_37127.cif" } resolution = 3.09 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 305 5.49 5 S 84 5.16 5 C 14835 2.51 5 N 4427 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24894 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3050 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 15, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 4498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4498 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 12, 'TRANS': 523} Chain breaks: 2 Chain: "D" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1535 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 1 Chain: "E" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2491 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain breaks: 5 Chain: "F" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 473 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain breaks: 1 Chain: "G" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 564 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain breaks: 2 Chain: "O" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 849 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 724 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "X" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "Y" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3100 Classifications: {'DNA': 152} Link IDs: {'rna3p': 151} Time building chain proxies: 5.42, per 1000 atoms: 0.22 Number of scatterers: 24894 At special positions: 0 Unit cell: (127.09, 166.85, 152.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 305 15.00 O 5243 8.00 N 4427 7.00 C 14835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 263 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 993.0 milliseconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4360 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 19 sheets defined 55.3% alpha, 3.4% beta 145 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 removed outlier: 3.622A pdb=" N VAL A 29 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 30' Processing helix chain 'A' and resid 42 through 54 removed outlier: 4.629A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 4.102A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.595A pdb=" N ILE A 83 " --> pdb=" O THR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.752A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.556A pdb=" N PHE A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 261 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.839A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 365 through 380 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.175A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.861A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 722 removed outlier: 3.694A pdb=" N ASN B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.597A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 840 removed outlier: 3.864A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN B 836 " --> pdb=" O GLU B 832 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS B 837 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.604A pdb=" N ALA B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 843 through 848' Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 874 through 886 removed outlier: 4.481A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 927 removed outlier: 3.643A pdb=" N LEU B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYS B 901 " --> pdb=" O ARG B 897 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 939 Processing helix chain 'B' and resid 944 through 961 removed outlier: 3.640A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 961 " --> pdb=" O VAL B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 999 removed outlier: 3.824A pdb=" N ASP B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU B 989 " --> pdb=" O PHE B 985 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 991 " --> pdb=" O ASP B 987 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 994 " --> pdb=" O CYS B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 4.182A pdb=" N LYS B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B1008 " --> pdb=" O ASN B1004 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 Processing helix chain 'B' and resid 1164 through 1172 Processing helix chain 'B' and resid 1202 through 1216 Processing helix chain 'B' and resid 1220 through 1232 Processing helix chain 'B' and resid 1237 through 1240 removed outlier: 3.709A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1237 through 1240' Processing helix chain 'B' and resid 1241 through 1255 Processing helix chain 'B' and resid 1259 through 1272 removed outlier: 3.550A pdb=" N ALA B1263 " --> pdb=" O ASP B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1282 through 1292 removed outlier: 3.596A pdb=" N TYR B1286 " --> pdb=" O ASP B1282 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B1292 " --> pdb=" O LEU B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1307 through 1310 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 254 through 265 removed outlier: 4.423A pdb=" N LYS D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 293 removed outlier: 4.431A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.545A pdb=" N ASP D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.611A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 369 removed outlier: 4.939A pdb=" N LEU D 354 " --> pdb=" O GLN D 350 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU D 355 " --> pdb=" O SER D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'E' and resid 52 through 57 Processing helix chain 'E' and resid 303 through 310 Processing helix chain 'E' and resid 321 through 325 removed outlier: 3.653A pdb=" N ASN E 325 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 330 Processing helix chain 'E' and resid 342 through 346 removed outlier: 4.078A pdb=" N HIS E 346 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 3.519A pdb=" N PHE E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 543 through 559 removed outlier: 3.680A pdb=" N LYS E 559 " --> pdb=" O ILE E 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 290 removed outlier: 4.293A pdb=" N SER F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.574A pdb=" N SER F 336 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 338 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 341 No H-bonds generated for 'chain 'F' and resid 339 through 341' Processing helix chain 'F' and resid 348 through 364 removed outlier: 3.615A pdb=" N PHE F 362 " --> pdb=" O GLN F 358 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 364 " --> pdb=" O GLU F 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 327 removed outlier: 3.912A pdb=" N ILE G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 334 Processing helix chain 'G' and resid 544 through 563 removed outlier: 4.271A pdb=" N ASP G 550 " --> pdb=" O SER G 546 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS G 563 " --> pdb=" O LYS G 559 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 74 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.778A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.074A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 27 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 3.974A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 4.349A pdb=" N ASP Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'R' and resid 52 through 81 removed outlier: 3.816A pdb=" N ASN R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.535A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 120 Processing helix chain 'S' and resid 44 through 55 Processing helix chain 'S' and resid 63 through 78 removed outlier: 3.512A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 Processing helix chain 'T' and resid 25 through 29 removed outlier: 3.734A pdb=" N ILE T 29 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 3.777A pdb=" N GLU T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA T 76 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 93 removed outlier: 3.525A pdb=" N VAL T 86 " --> pdb=" O THR T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 removed outlier: 3.510A pdb=" N ARG U 20 " --> pdb=" O THR U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 45 through 72 removed outlier: 4.178A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP U 72 " --> pdb=" O ASN U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.587A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'V' and resid 52 through 81 Processing helix chain 'V' and resid 87 through 99 removed outlier: 3.559A pdb=" N ILE V 91 " --> pdb=" O THR V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.278A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA V 107 " --> pdb=" O LEU V 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 7.996A pdb=" N VAL A 21 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N TYR A 64 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 23 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 185 removed outlier: 7.288A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 756 through 757 removed outlier: 3.780A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id=AA5, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA6, first strand: chain 'E' and resid 272 through 274 Processing sheet with id=AA7, first strand: chain 'E' and resid 365 through 366 removed outlier: 3.694A pdb=" N LYS E 365 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AA9, first strand: chain 'E' and resid 520 through 522 removed outlier: 5.823A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 83 through 84 removed outlier: 7.348A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 118 through 119 removed outlier: 3.641A pdb=" N ILE O 119 " --> pdb=" O ARG P 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.256A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.372A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'Q' and resid 100 through 101 Processing sheet with id=AB7, first strand: chain 'S' and resid 83 through 84 removed outlier: 7.026A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB9, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.225A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 77 through 78 842 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 7.55 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6907 1.34 - 1.46: 7590 1.46 - 1.58: 10780 1.58 - 1.71: 610 1.71 - 1.83: 129 Bond restraints: 26016 Sorted by residual: bond pdb=" N PRO S 38 " pdb=" CD PRO S 38 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" CB PRO B 766 " pdb=" CG PRO B 766 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.21e+01 bond pdb=" CG PRO B 766 " pdb=" CD PRO B 766 " ideal model delta sigma weight residual 1.503 1.385 0.118 3.40e-02 8.65e+02 1.20e+01 bond pdb=" CB ASP B 772 " pdb=" CG ASP B 772 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.35e+00 bond pdb=" N PRO B 766 " pdb=" CD PRO B 766 " ideal model delta sigma weight residual 1.473 1.504 -0.031 1.40e-02 5.10e+03 4.85e+00 ... (remaining 26011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 36208 4.47 - 8.95: 173 8.95 - 13.42: 25 13.42 - 17.90: 12 17.90 - 22.37: 1 Bond angle restraints: 36419 Sorted by residual: angle pdb=" CA PRO B 766 " pdb=" N PRO B 766 " pdb=" CD PRO B 766 " ideal model delta sigma weight residual 112.00 95.47 16.53 1.40e+00 5.10e-01 1.39e+02 angle pdb=" CA LEU D 386 " pdb=" CB LEU D 386 " pdb=" CG LEU D 386 " ideal model delta sigma weight residual 116.30 138.67 -22.37 3.50e+00 8.16e-02 4.09e+01 angle pdb=" CB MET F 296 " pdb=" CG MET F 296 " pdb=" SD MET F 296 " ideal model delta sigma weight residual 112.70 130.22 -17.52 3.00e+00 1.11e-01 3.41e+01 angle pdb=" N PRO B 766 " pdb=" CD PRO B 766 " pdb=" CG PRO B 766 " ideal model delta sigma weight residual 103.20 94.93 8.27 1.50e+00 4.44e-01 3.04e+01 angle pdb=" CB MET B1266 " pdb=" CG MET B1266 " pdb=" SD MET B1266 " ideal model delta sigma weight residual 112.70 129.14 -16.44 3.00e+00 1.11e-01 3.00e+01 ... (remaining 36414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 13087 35.57 - 71.13: 1737 71.13 - 106.70: 63 106.70 - 142.26: 0 142.26 - 177.83: 1 Dihedral angle restraints: 14888 sinusoidal: 8147 harmonic: 6741 Sorted by residual: dihedral pdb=" CB CYS E 303 " pdb=" SG CYS E 303 " pdb=" SG CYS E 306 " pdb=" CB CYS E 306 " ideal model delta sinusoidal sigma weight residual 93.00 171.39 -78.39 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CA MET B 765 " pdb=" C MET B 765 " pdb=" N PRO B 766 " pdb=" CA PRO B 766 " ideal model delta harmonic sigma weight residual -180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLU B1171 " pdb=" C GLU B1171 " pdb=" N ILE B1172 " pdb=" CA ILE B1172 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 14885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3777 0.087 - 0.173: 242 0.173 - 0.260: 13 0.260 - 0.347: 3 0.347 - 0.433: 2 Chirality restraints: 4037 Sorted by residual: chirality pdb=" CG LEU D 363 " pdb=" CB LEU D 363 " pdb=" CD1 LEU D 363 " pdb=" CD2 LEU D 363 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CG LEU O 48 " pdb=" CB LEU O 48 " pdb=" CD1 LEU O 48 " pdb=" CD2 LEU O 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB VAL A 268 " pdb=" CA VAL A 268 " pdb=" CG1 VAL A 268 " pdb=" CG2 VAL A 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 4034 not shown) Planarity restraints: 3566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 336 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.51e+01 pdb=" C SER F 336 " 0.103 2.00e-02 2.50e+03 pdb=" O SER F 336 " -0.038 2.00e-02 2.50e+03 pdb=" N VAL F 337 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 765 " 0.107 5.00e-02 4.00e+02 1.47e-01 3.46e+01 pdb=" N PRO B 766 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO B 766 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO B 766 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 507 " -0.081 5.00e-02 4.00e+02 1.24e-01 2.48e+01 pdb=" N PRO E 508 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO E 508 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO E 508 " -0.066 5.00e-02 4.00e+02 ... (remaining 3563 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 36 2.39 - 3.02: 12184 3.02 - 3.65: 41723 3.65 - 4.27: 60541 4.27 - 4.90: 92190 Nonbonded interactions: 206674 Sorted by model distance: nonbonded pdb=" NE2 HIS A 188 " pdb=" OD2 ASP A 274 " model vdw 1.768 3.120 nonbonded pdb=" O ASN T 25 " pdb=" OD1 ASN T 25 " model vdw 2.169 3.040 nonbonded pdb=" CE1 HIS A 188 " pdb=" OD2 ASP A 274 " model vdw 2.247 3.260 nonbonded pdb=" OD1 ASP A 243 " pdb=" OG1 THR A 246 " model vdw 2.267 3.040 nonbonded pdb=" O LEU O 103 " pdb=" OG1 THR O 107 " model vdw 2.274 3.040 ... (remaining 206669 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'O' and resid 36 through 133) selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = (chain 'V' and resid 29 through 119) } 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=0.00 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: 18.970 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: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.750 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.004 0.174 26018 Z= 0.196 Angle : 0.880 22.370 36423 Z= 0.460 Chirality : 0.046 0.433 4037 Planarity : 0.007 0.147 3566 Dihedral : 24.430 177.831 10522 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.25 % Allowed : 31.86 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2243 helix: -0.61 (0.14), residues: 1171 sheet: -1.11 (0.60), residues: 86 loop : -1.85 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG V 96 TYR 0.035 0.001 TYR A 58 PHE 0.061 0.002 PHE E 326 TRP 0.027 0.001 TRP D 236 HIS 0.023 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00416 (26016) covalent geometry : angle 0.87980 (36419) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.41701 ( 4) hydrogen bonds : bond 0.12461 ( 1213) hydrogen bonds : angle 5.40119 ( 3204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 300 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.6260 (tpp) cc_final: 0.5516 (tmm) REVERT: A 365 THR cc_start: 0.6652 (p) cc_final: 0.6306 (t) REVERT: B 1020 LEU cc_start: 0.6256 (pp) cc_final: 0.5796 (mm) REVERT: B 1226 GLU cc_start: 0.5485 (mt-10) cc_final: 0.5090 (pt0) REVERT: D 243 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7450 (tttt) REVERT: V 61 SER cc_start: 0.9071 (p) cc_final: 0.8761 (m) outliers start: 5 outliers final: 3 residues processed: 302 average time/residue: 0.1595 time to fit residues: 78.0215 Evaluate side-chains 264 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain S residue 37 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN B 947 GLN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN E 65 ASN E 283 HIS E 448 HIS E 541 GLN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 ASN ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN O 113 HIS Q 38 ASN R 46 HIS R 79 HIS S 39 HIS ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.129429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.100373 restraints weight = 65479.504| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.06 r_work: 0.3395 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 26018 Z= 0.293 Angle : 0.740 11.856 36423 Z= 0.396 Chirality : 0.044 0.227 4037 Planarity : 0.005 0.084 3566 Dihedral : 26.987 178.698 5863 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.25 % Allowed : 25.14 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2243 helix: -0.01 (0.14), residues: 1176 sheet: -0.98 (0.62), residues: 75 loop : -1.59 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 96 TYR 0.041 0.002 TYR S 54 PHE 0.035 0.002 PHE B1017 TRP 0.030 0.002 TRP E 301 HIS 0.010 0.002 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00668 (26016) covalent geometry : angle 0.74019 (36419) SS BOND : bond 0.00472 ( 2) SS BOND : angle 1.99393 ( 4) hydrogen bonds : bond 0.04956 ( 1213) hydrogen bonds : angle 4.04540 ( 3204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 303 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 204 MET cc_start: 0.7395 (tmm) cc_final: 0.7084 (tmm) REVERT: A 340 TYR cc_start: 0.6693 (p90) cc_final: 0.6142 (p90) REVERT: B 912 TRP cc_start: 0.8591 (m100) cc_final: 0.8259 (m100) REVERT: B 920 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 1194 MET cc_start: 0.6164 (mpm) cc_final: 0.5856 (mpm) REVERT: B 1199 VAL cc_start: 0.4318 (OUTLIER) cc_final: 0.4078 (p) REVERT: D 311 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7846 (tptp) REVERT: D 356 ILE cc_start: 0.8495 (mp) cc_final: 0.8276 (mm) REVERT: D 395 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7859 (mt-10) REVERT: E 61 ARG cc_start: 0.7099 (ppt170) cc_final: 0.6400 (tpp-160) REVERT: E 283 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6957 (m-70) REVERT: E 400 SER cc_start: 0.7196 (OUTLIER) cc_final: 0.6985 (t) REVERT: E 448 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.6540 (m90) REVERT: E 541 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7553 (mm-40) REVERT: F 296 MET cc_start: 0.5284 (ppp) cc_final: 0.4917 (ppp) REVERT: G 331 ASN cc_start: 0.4277 (OUTLIER) cc_final: 0.3995 (m110) REVERT: O 54 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.6798 (t80) REVERT: O 64 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8376 (mttt) REVERT: P 59 LYS cc_start: 0.9117 (tttt) cc_final: 0.8913 (tttp) REVERT: Q 56 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: S 125 GLN cc_start: 0.8835 (mt0) cc_final: 0.8500 (mt0) REVERT: S 129 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7304 (tmm160) outliers start: 107 outliers final: 50 residues processed: 374 average time/residue: 0.1826 time to fit residues: 105.3493 Evaluate side-chains 325 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 916 TRP Chi-restraints excluded: chain B residue 1166 GLU Chi-restraints excluded: chain B residue 1199 VAL Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 400 SER Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 448 HIS Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 541 GLN Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 328 LYS Chi-restraints excluded: chain G residue 331 ASN Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain S residue 129 ARG Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN D 295 ASN D 389 ASN E 283 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN G 325 ASN G 332 ASN R 46 HIS R 60 ASN R 64 ASN R 81 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.130144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.101284 restraints weight = 65401.066| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.02 r_work: 0.3423 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26018 Z= 0.173 Angle : 0.601 12.243 36423 Z= 0.328 Chirality : 0.038 0.196 4037 Planarity : 0.004 0.066 3566 Dihedral : 26.871 175.523 5857 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.07 % Allowed : 26.12 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2243 helix: 0.48 (0.15), residues: 1184 sheet: -0.27 (0.66), residues: 57 loop : -1.46 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 52 TYR 0.028 0.002 TYR O 54 PHE 0.020 0.001 PHE E 311 TRP 0.030 0.001 TRP D 365 HIS 0.019 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00385 (26016) covalent geometry : angle 0.60089 (36419) SS BOND : bond 0.00432 ( 2) SS BOND : angle 1.97013 ( 4) hydrogen bonds : bond 0.03849 ( 1213) hydrogen bonds : angle 3.67197 ( 3204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 285 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6748 (t80) REVERT: A 204 MET cc_start: 0.7499 (tmm) cc_final: 0.6904 (tmm) REVERT: A 325 GLU cc_start: 0.8027 (tp30) cc_final: 0.7796 (tp30) REVERT: A 340 TYR cc_start: 0.7016 (p90) cc_final: 0.6428 (p90) REVERT: A 373 MET cc_start: 0.7248 (mmt) cc_final: 0.7032 (mmp) REVERT: B 920 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8494 (mm-30) REVERT: B 1194 MET cc_start: 0.6375 (mpm) cc_final: 0.5742 (mpm) REVERT: D 256 MET cc_start: 0.7373 (mpt) cc_final: 0.6476 (mpp) REVERT: D 263 HIS cc_start: 0.6585 (OUTLIER) cc_final: 0.6161 (p90) REVERT: D 295 ASN cc_start: 0.7354 (m-40) cc_final: 0.7095 (t0) REVERT: D 311 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7971 (tptp) REVERT: D 386 LEU cc_start: 0.8409 (tm) cc_final: 0.7890 (pp) REVERT: D 393 GLN cc_start: 0.8145 (tp40) cc_final: 0.7915 (tp40) REVERT: E 35 ARG cc_start: 0.7076 (tmm-80) cc_final: 0.5879 (ptp-170) REVERT: E 61 ARG cc_start: 0.7121 (ppt170) cc_final: 0.6367 (tpp-160) REVERT: E 283 HIS cc_start: 0.6726 (m90) cc_final: 0.6346 (m-70) REVERT: E 371 GLN cc_start: 0.8483 (mp10) cc_final: 0.8022 (pm20) REVERT: E 436 LEU cc_start: 0.7790 (tp) cc_final: 0.7211 (mp) REVERT: E 537 PHE cc_start: 0.4108 (OUTLIER) cc_final: 0.3406 (t80) REVERT: E 541 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7307 (mm110) REVERT: F 296 MET cc_start: 0.5586 (ppp) cc_final: 0.5062 (ppp) REVERT: O 54 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7051 (t80) REVERT: O 64 LYS cc_start: 0.8719 (mptt) cc_final: 0.8505 (mttt) REVERT: Q 56 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8679 (tt0) outliers start: 83 outliers final: 50 residues processed: 340 average time/residue: 0.1738 time to fit residues: 92.8658 Evaluate side-chains 317 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1262 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 541 GLN Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain V residue 83 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 89 optimal weight: 8.9990 chunk 185 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 197 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 HIS ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.129641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.100828 restraints weight = 64724.682| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.95 r_work: 0.3423 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26018 Z= 0.163 Angle : 0.587 10.832 36423 Z= 0.321 Chirality : 0.038 0.214 4037 Planarity : 0.004 0.055 3566 Dihedral : 26.793 176.806 5857 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.61 % Allowed : 25.23 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2243 helix: 0.65 (0.15), residues: 1191 sheet: -1.22 (0.60), residues: 74 loop : -1.26 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 52 TYR 0.027 0.002 TYR E 46 PHE 0.011 0.001 PHE A 24 TRP 0.028 0.001 TRP D 365 HIS 0.011 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00366 (26016) covalent geometry : angle 0.58658 (36419) SS BOND : bond 0.00440 ( 2) SS BOND : angle 2.00748 ( 4) hydrogen bonds : bond 0.03698 ( 1213) hydrogen bonds : angle 3.55832 ( 3204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 277 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6790 (t80) REVERT: A 325 GLU cc_start: 0.8073 (tp30) cc_final: 0.7858 (tp30) REVERT: A 340 TYR cc_start: 0.6946 (p90) cc_final: 0.6295 (p90) REVERT: B 920 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8478 (mm-30) REVERT: D 256 MET cc_start: 0.7543 (mpt) cc_final: 0.6545 (mpp) REVERT: D 263 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.6244 (p90) REVERT: D 295 ASN cc_start: 0.7523 (m-40) cc_final: 0.7134 (t0) REVERT: D 311 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8018 (tptp) REVERT: D 360 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8548 (pt0) REVERT: E 35 ARG cc_start: 0.7052 (tmm-80) cc_final: 0.5856 (ptp-170) REVERT: E 61 ARG cc_start: 0.7083 (ppt170) cc_final: 0.6356 (tpp-160) REVERT: E 283 HIS cc_start: 0.7168 (m90) cc_final: 0.6828 (m-70) REVERT: E 346 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7408 (m-70) REVERT: E 436 LEU cc_start: 0.7821 (tp) cc_final: 0.7291 (mp) REVERT: E 537 PHE cc_start: 0.4367 (OUTLIER) cc_final: 0.3665 (t80) REVERT: E 541 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7486 (mm-40) REVERT: E 549 TYR cc_start: 0.6165 (m-80) cc_final: 0.5840 (m-80) REVERT: F 296 MET cc_start: 0.5760 (ppp) cc_final: 0.5351 (ppp) REVERT: O 54 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.6924 (t80) REVERT: Q 56 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: T 84 MET cc_start: 0.9039 (tpp) cc_final: 0.8835 (mmt) REVERT: T 95 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8582 (ttm-80) outliers start: 94 outliers final: 53 residues processed: 338 average time/residue: 0.1672 time to fit residues: 89.4373 Evaluate side-chains 318 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1137 ASN Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 541 GLN Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain T residue 95 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 83 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 248 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 141 optimal weight: 0.0170 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 214 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN E 448 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.127814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.099879 restraints weight = 64839.308| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.91 r_work: 0.3373 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26018 Z= 0.184 Angle : 0.603 12.126 36423 Z= 0.329 Chirality : 0.039 0.222 4037 Planarity : 0.004 0.062 3566 Dihedral : 26.897 177.247 5857 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.91 % Allowed : 25.04 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2243 helix: 0.65 (0.15), residues: 1208 sheet: -1.26 (0.57), residues: 77 loop : -1.23 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 52 TYR 0.032 0.002 TYR A 420 PHE 0.020 0.001 PHE E 311 TRP 0.022 0.001 TRP D 365 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00416 (26016) covalent geometry : angle 0.60281 (36419) SS BOND : bond 0.00281 ( 2) SS BOND : angle 1.93470 ( 4) hydrogen bonds : bond 0.03791 ( 1213) hydrogen bonds : angle 3.55940 ( 3204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 283 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 PHE cc_start: 0.7816 (p90) cc_final: 0.7564 (p90) REVERT: A 204 MET cc_start: 0.6903 (tmm) cc_final: 0.6654 (ttt) REVERT: A 306 MET cc_start: 0.8322 (tmt) cc_final: 0.7849 (tmt) REVERT: A 340 TYR cc_start: 0.6787 (p90) cc_final: 0.6155 (p90) REVERT: B 900 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: B 920 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8358 (mm-30) REVERT: D 256 MET cc_start: 0.7617 (mpt) cc_final: 0.6860 (mpp) REVERT: D 263 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.6345 (p90) REVERT: D 295 ASN cc_start: 0.7560 (m-40) cc_final: 0.7190 (t0) REVERT: D 311 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8156 (tptp) REVERT: D 360 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: E 35 ARG cc_start: 0.6994 (tmm-80) cc_final: 0.5782 (ptp-170) REVERT: E 283 HIS cc_start: 0.7316 (m90) cc_final: 0.6956 (m-70) REVERT: E 346 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7428 (m-70) REVERT: E 436 LEU cc_start: 0.7776 (tp) cc_final: 0.7268 (mp) REVERT: E 537 PHE cc_start: 0.4135 (OUTLIER) cc_final: 0.3498 (t80) REVERT: E 541 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7553 (mm110) REVERT: E 549 TYR cc_start: 0.6106 (m-80) cc_final: 0.5784 (m-80) REVERT: F 296 MET cc_start: 0.6009 (ppp) cc_final: 0.5797 (ppp) REVERT: O 42 ARG cc_start: 0.8837 (mtt-85) cc_final: 0.8455 (mmt90) REVERT: O 54 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6764 (t80) REVERT: O 93 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.7974 (tp-100) REVERT: Q 56 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8375 (tt0) outliers start: 100 outliers final: 66 residues processed: 351 average time/residue: 0.1619 time to fit residues: 90.9941 Evaluate side-chains 334 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 258 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1262 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 541 GLN Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain S residue 41 TYR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 83 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 33 optimal weight: 0.0020 chunk 96 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 175 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 211 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1234 ASN D 393 GLN E 302 HIS E 448 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.129710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.101685 restraints weight = 64815.414| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.16 r_work: 0.3392 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26018 Z= 0.139 Angle : 0.581 11.398 36423 Z= 0.317 Chirality : 0.038 0.241 4037 Planarity : 0.004 0.064 3566 Dihedral : 26.730 176.717 5857 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.17 % Allowed : 25.72 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2243 helix: 0.79 (0.15), residues: 1205 sheet: -1.15 (0.60), residues: 74 loop : -1.17 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 52 TYR 0.034 0.001 TYR E 46 PHE 0.010 0.001 PHE A 24 TRP 0.036 0.002 TRP E 492 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00305 (26016) covalent geometry : angle 0.58068 (36419) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.90624 ( 4) hydrogen bonds : bond 0.03518 ( 1213) hydrogen bonds : angle 3.45064 ( 3204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 285 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7132 (tmm) cc_final: 0.6673 (ttt) REVERT: A 306 MET cc_start: 0.8265 (tmt) cc_final: 0.7855 (tmt) REVERT: A 340 TYR cc_start: 0.6883 (p90) cc_final: 0.6216 (p90) REVERT: B 900 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: B 920 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8365 (mm-30) REVERT: D 243 LYS cc_start: 0.7550 (tttt) cc_final: 0.7278 (tttt) REVERT: D 256 MET cc_start: 0.7656 (mpt) cc_final: 0.6822 (mpp) REVERT: D 263 HIS cc_start: 0.6710 (OUTLIER) cc_final: 0.6357 (p90) REVERT: D 295 ASN cc_start: 0.7577 (m-40) cc_final: 0.7206 (t0) REVERT: D 311 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8120 (tptp) REVERT: D 360 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: D 393 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7625 (tp40) REVERT: E 283 HIS cc_start: 0.7246 (m90) cc_final: 0.6867 (m-70) REVERT: E 340 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7889 (mm) REVERT: E 346 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7317 (m-70) REVERT: E 418 TYR cc_start: 0.6536 (t80) cc_final: 0.6279 (t80) REVERT: E 436 LEU cc_start: 0.7814 (tp) cc_final: 0.7345 (mp) REVERT: E 537 PHE cc_start: 0.4337 (OUTLIER) cc_final: 0.3711 (t80) REVERT: O 42 ARG cc_start: 0.8854 (mtt-85) cc_final: 0.8472 (mmt90) REVERT: O 54 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6652 (t80) REVERT: O 93 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8053 (tp-100) REVERT: Q 56 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8377 (tt0) outliers start: 85 outliers final: 54 residues processed: 341 average time/residue: 0.1590 time to fit residues: 87.3552 Evaluate side-chains 324 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 900 GLN Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1137 ASN Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1262 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 495 GLN Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 74 ILE Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain S residue 41 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 66 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN B1234 ASN ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN E 302 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN T 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.124902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.095384 restraints weight = 64206.219| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.00 r_work: 0.3311 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26018 Z= 0.238 Angle : 0.650 11.258 36423 Z= 0.353 Chirality : 0.042 0.254 4037 Planarity : 0.004 0.064 3566 Dihedral : 27.181 179.171 5857 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.76 % Allowed : 25.23 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2243 helix: 0.54 (0.14), residues: 1229 sheet: -1.11 (0.57), residues: 82 loop : -1.29 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 136 TYR 0.042 0.002 TYR P 88 PHE 0.022 0.002 PHE A 284 TRP 0.027 0.002 TRP E 492 HIS 0.018 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00545 (26016) covalent geometry : angle 0.64954 (36419) SS BOND : bond 0.00343 ( 2) SS BOND : angle 1.97699 ( 4) hydrogen bonds : bond 0.04221 ( 1213) hydrogen bonds : angle 3.68549 ( 3204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 268 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7151 (t0) cc_final: 0.6507 (m-30) REVERT: A 204 MET cc_start: 0.7449 (tmm) cc_final: 0.7017 (ttt) REVERT: A 306 MET cc_start: 0.8555 (tmt) cc_final: 0.8297 (tmt) REVERT: A 340 TYR cc_start: 0.7208 (p90) cc_final: 0.6489 (p90) REVERT: B 841 MET cc_start: 0.3063 (ptp) cc_final: 0.2483 (pmm) REVERT: B 920 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8393 (mm-30) REVERT: B 1015 LYS cc_start: 0.7639 (mmtt) cc_final: 0.6557 (tmtt) REVERT: D 256 MET cc_start: 0.7845 (mpt) cc_final: 0.7045 (mpp) REVERT: D 263 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6461 (p90) REVERT: D 295 ASN cc_start: 0.7597 (m-40) cc_final: 0.6994 (t0) REVERT: D 311 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8295 (tptp) REVERT: D 360 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8536 (pt0) REVERT: E 283 HIS cc_start: 0.7490 (m90) cc_final: 0.6862 (m90) REVERT: E 346 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7327 (m-70) REVERT: E 436 LEU cc_start: 0.8026 (tp) cc_final: 0.7570 (mp) REVERT: E 505 TYR cc_start: 0.8327 (m-10) cc_final: 0.7998 (m-10) REVERT: E 537 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.4017 (t80) REVERT: E 541 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: E 549 TYR cc_start: 0.6252 (m-80) cc_final: 0.5831 (m-10) REVERT: O 54 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.6950 (t80) REVERT: O 93 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.7979 (tp-100) REVERT: Q 56 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8617 (tt0) outliers start: 97 outliers final: 69 residues processed: 333 average time/residue: 0.1575 time to fit residues: 84.6584 Evaluate side-chains 340 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 262 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1137 ASN Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1262 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 495 GLN Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 541 GLN Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain V residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 123 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 206 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN D 393 GLN E 302 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.127512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.098644 restraints weight = 64476.743| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.94 r_work: 0.3385 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26018 Z= 0.152 Angle : 0.608 11.820 36423 Z= 0.331 Chirality : 0.039 0.274 4037 Planarity : 0.004 0.065 3566 Dihedral : 26.874 176.429 5857 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.78 % Allowed : 26.41 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2243 helix: 0.72 (0.15), residues: 1211 sheet: -1.24 (0.57), residues: 77 loop : -1.20 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.023 0.002 TYR O 54 PHE 0.013 0.001 PHE A 113 TRP 0.043 0.002 TRP D 365 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00339 (26016) covalent geometry : angle 0.60805 (36419) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.82601 ( 4) hydrogen bonds : bond 0.03652 ( 1213) hydrogen bonds : angle 3.54471 ( 3204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 280 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7118 (t0) cc_final: 0.6541 (m-30) REVERT: A 204 MET cc_start: 0.7399 (tmm) cc_final: 0.6994 (ttt) REVERT: A 340 TYR cc_start: 0.7074 (p90) cc_final: 0.6353 (p90) REVERT: B 817 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6843 (t80) REVERT: B 841 MET cc_start: 0.2885 (ptp) cc_final: 0.2455 (pmm) REVERT: B 920 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 946 LYS cc_start: 0.7791 (pttt) cc_final: 0.7536 (ptpt) REVERT: B 1015 LYS cc_start: 0.7594 (mmtt) cc_final: 0.6533 (tmtt) REVERT: D 256 MET cc_start: 0.7866 (mpt) cc_final: 0.6819 (mpp) REVERT: D 263 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.6610 (p90) REVERT: D 295 ASN cc_start: 0.7524 (m-40) cc_final: 0.7085 (t0) REVERT: D 311 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8305 (tptp) REVERT: D 360 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: E 283 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6906 (m90) REVERT: E 346 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7388 (m-70) REVERT: E 436 LEU cc_start: 0.7989 (tp) cc_final: 0.7514 (mp) REVERT: E 537 PHE cc_start: 0.4572 (OUTLIER) cc_final: 0.4014 (t80) REVERT: O 42 ARG cc_start: 0.8918 (mtt-85) cc_final: 0.8528 (mmt90) REVERT: O 54 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.6849 (t80) REVERT: O 73 GLU cc_start: 0.8532 (tt0) cc_final: 0.8316 (tt0) REVERT: O 93 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8081 (tp-100) REVERT: Q 56 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8592 (tt0) outliers start: 77 outliers final: 61 residues processed: 328 average time/residue: 0.1629 time to fit residues: 85.1101 Evaluate side-chains 340 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1137 ASN Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1262 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 41 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 83 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 189 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN D 393 GLN E 42 GLN E 302 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN T 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.126278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.097461 restraints weight = 64426.733| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.91 r_work: 0.3358 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26018 Z= 0.181 Angle : 0.622 11.161 36423 Z= 0.338 Chirality : 0.040 0.268 4037 Planarity : 0.004 0.065 3566 Dihedral : 26.916 178.094 5857 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.07 % Allowed : 25.92 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2243 helix: 0.68 (0.15), residues: 1213 sheet: -1.22 (0.57), residues: 77 loop : -1.19 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 136 TYR 0.034 0.002 TYR A 420 PHE 0.023 0.001 PHE E 311 TRP 0.072 0.002 TRP D 365 HIS 0.011 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00410 (26016) covalent geometry : angle 0.62215 (36419) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.81216 ( 4) hydrogen bonds : bond 0.03762 ( 1213) hydrogen bonds : angle 3.60594 ( 3204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ILE cc_start: 0.8441 (mm) cc_final: 0.8177 (mt) REVERT: A 109 ASP cc_start: 0.7149 (t0) cc_final: 0.6608 (m-30) REVERT: A 204 MET cc_start: 0.7576 (tmm) cc_final: 0.7359 (tmm) REVERT: A 340 TYR cc_start: 0.7112 (p90) cc_final: 0.6369 (p90) REVERT: B 817 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6874 (t80) REVERT: B 841 MET cc_start: 0.3088 (ptp) cc_final: 0.2641 (pmm) REVERT: B 912 TRP cc_start: 0.8850 (m100) cc_final: 0.8333 (m100) REVERT: B 920 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8385 (mm-30) REVERT: B 1015 LYS cc_start: 0.7778 (mmtt) cc_final: 0.6691 (tmtt) REVERT: D 238 TYR cc_start: 0.7966 (m-80) cc_final: 0.7612 (m-80) REVERT: D 263 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6579 (p90) REVERT: D 295 ASN cc_start: 0.7567 (m-40) cc_final: 0.7250 (t0) REVERT: D 311 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8332 (tptp) REVERT: D 360 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: E 35 ARG cc_start: 0.6971 (tmm-80) cc_final: 0.5747 (ptp-170) REVERT: E 50 ARG cc_start: 0.5984 (mtm-85) cc_final: 0.5410 (mtt-85) REVERT: E 283 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6883 (m90) REVERT: E 346 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7342 (m-70) REVERT: E 436 LEU cc_start: 0.8028 (tp) cc_final: 0.7583 (mp) REVERT: E 537 PHE cc_start: 0.4735 (OUTLIER) cc_final: 0.3987 (t80) REVERT: E 549 TYR cc_start: 0.6252 (m-80) cc_final: 0.5791 (m-10) REVERT: O 42 ARG cc_start: 0.8950 (mtt-85) cc_final: 0.8552 (mmt90) REVERT: O 54 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6821 (t80) REVERT: O 93 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8070 (tp-100) REVERT: Q 56 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: V 39 TYR cc_start: 0.8514 (t80) cc_final: 0.8133 (t80) outliers start: 83 outliers final: 63 residues processed: 335 average time/residue: 0.1733 time to fit residues: 91.1397 Evaluate side-chains 343 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 270 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1137 ASN Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1262 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 41 TYR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 117 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 chunk 138 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 179 optimal weight: 2.9990 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 389 ASN E 302 HIS E 519 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.126372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.097551 restraints weight = 64422.331| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.92 r_work: 0.3356 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26018 Z= 0.176 Angle : 0.632 11.411 36423 Z= 0.342 Chirality : 0.040 0.322 4037 Planarity : 0.004 0.066 3566 Dihedral : 26.886 177.819 5857 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.88 % Allowed : 26.12 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2243 helix: 0.67 (0.15), residues: 1220 sheet: -1.15 (0.58), residues: 77 loop : -1.19 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 136 TYR 0.025 0.002 TYR O 54 PHE 0.016 0.001 PHE A 284 TRP 0.063 0.002 TRP E 492 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00396 (26016) covalent geometry : angle 0.63149 (36419) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.80059 ( 4) hydrogen bonds : bond 0.03717 ( 1213) hydrogen bonds : angle 3.59917 ( 3204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 280 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7231 (t0) cc_final: 0.6710 (m-30) REVERT: A 340 TYR cc_start: 0.7104 (p90) cc_final: 0.6353 (p90) REVERT: B 817 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6921 (t80) REVERT: B 841 MET cc_start: 0.3211 (ptp) cc_final: 0.2738 (pmm) REVERT: B 912 TRP cc_start: 0.8847 (m100) cc_final: 0.8312 (m100) REVERT: B 920 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 1015 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7373 (mmtt) REVERT: D 238 TYR cc_start: 0.7803 (m-80) cc_final: 0.7415 (m-80) REVERT: D 295 ASN cc_start: 0.7627 (m-40) cc_final: 0.7239 (t0) REVERT: D 311 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8345 (tptp) REVERT: D 360 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: E 35 ARG cc_start: 0.6880 (tmm-80) cc_final: 0.5726 (ptp-170) REVERT: E 50 ARG cc_start: 0.5997 (mtm-85) cc_final: 0.5418 (mtt-85) REVERT: E 283 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6881 (m90) REVERT: E 346 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7357 (m-70) REVERT: E 436 LEU cc_start: 0.8003 (tp) cc_final: 0.7558 (mp) REVERT: E 537 PHE cc_start: 0.4698 (OUTLIER) cc_final: 0.4267 (t80) REVERT: E 549 TYR cc_start: 0.6192 (m-80) cc_final: 0.5753 (m-10) REVERT: G 329 GLN cc_start: 0.7470 (pm20) cc_final: 0.6232 (mm-40) REVERT: O 42 ARG cc_start: 0.8937 (mtt-85) cc_final: 0.8530 (mmt90) REVERT: O 54 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.6828 (t80) REVERT: O 93 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8074 (tp-100) REVERT: Q 56 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: V 39 TYR cc_start: 0.8527 (t80) cc_final: 0.8137 (t80) outliers start: 79 outliers final: 63 residues processed: 330 average time/residue: 0.1662 time to fit residues: 86.7806 Evaluate side-chains 341 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1137 ASN Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1262 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 41 TYR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 153 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 202 optimal weight: 0.0050 chunk 56 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN E 302 HIS ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.128155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.099636 restraints weight = 64348.767| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.92 r_work: 0.3407 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26018 Z= 0.146 Angle : 0.621 13.066 36423 Z= 0.334 Chirality : 0.039 0.317 4037 Planarity : 0.004 0.066 3566 Dihedral : 26.718 177.661 5857 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.44 % Allowed : 26.41 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2243 helix: 0.78 (0.15), residues: 1230 sheet: -0.93 (0.60), residues: 77 loop : -1.20 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 136 TYR 0.034 0.001 TYR A 420 PHE 0.024 0.001 PHE E 311 TRP 0.062 0.002 TRP E 492 HIS 0.007 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00325 (26016) covalent geometry : angle 0.62107 (36419) SS BOND : bond 0.00281 ( 2) SS BOND : angle 1.74523 ( 4) hydrogen bonds : bond 0.03542 ( 1213) hydrogen bonds : angle 3.51559 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8573.87 seconds wall clock time: 146 minutes 48.62 seconds (8808.62 seconds total)