Starting phenix.real_space_refine on Sun May 25 08:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd5_37125/05_2025/8kd5_37125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd5_37125/05_2025/8kd5_37125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd5_37125/05_2025/8kd5_37125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd5_37125/05_2025/8kd5_37125.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd5_37125/05_2025/8kd5_37125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd5_37125/05_2025/8kd5_37125.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 319 5.49 5 S 91 5.16 5 C 16088 2.51 5 N 4778 2.21 5 O 5631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26908 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 2 Chain: "F" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1573 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 2 Chain: "O" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} 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: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3277 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "Y" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3261 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4519 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 12, 'TRANS': 526} Chain breaks: 2 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2611 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain breaks: 3 Chain: "G" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 724 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.92, per 1000 atoms: 0.63 Number of scatterers: 26908 At special positions: 0 Unit cell: (139.87, 152.65, 188.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 91 16.00 P 319 15.00 O 5631 8.00 N 4778 7.00 C 16088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 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: 5.75 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 19 sheets defined 59.0% alpha, 3.8% beta 133 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 10.24 Creating SS restraints... Processing helix chain 'D' and resid 98 through 112 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.911A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 293 removed outlier: 4.425A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 316 removed outlier: 4.505A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.525A pdb=" N ARG D 324 " --> pdb=" O VAL D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 343 removed outlier: 3.914A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'F' and resid 98 through 112 removed outlier: 3.796A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 4.408A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 removed outlier: 4.192A pdb=" N VAL F 257 " --> pdb=" O THR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 265 removed outlier: 3.721A pdb=" N VAL F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 290 removed outlier: 4.374A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 313 Processing helix chain 'F' and resid 329 through 338 removed outlier: 4.319A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.817A pdb=" N SER F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 369 removed outlier: 3.889A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS F 369 " --> pdb=" O TRP F 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.734A 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: 3.790A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.344A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 3.606A pdb=" N LEU Q 83 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) removed outlier: 3.507A 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 removed outlier: 3.622A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 81 removed outlier: 3.538A pdb=" N TYR R 80 " --> pdb=" O ARG R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 99 Processing helix chain 'R' and resid 101 through 120 removed outlier: 3.521A pdb=" N HIS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.567A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.640A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.893A 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: 3.826A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.036A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.538A 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 removed outlier: 3.511A pdb=" N VAL V 38 " --> pdb=" O TYR V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.642A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.133A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS V 106 " --> pdb=" O GLU V 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.830A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.846A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.670A pdb=" N LEU A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.868A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 104' Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.645A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.747A pdb=" N GLU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.007A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 removed outlier: 3.723A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.524A pdb=" N TYR A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.459A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.928A 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: 3.628A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 Processing helix chain 'B' and resid 801 through 840 removed outlier: 3.788A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.937A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.504A pdb=" N TYR B 871 " --> pdb=" O ILE B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.749A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 4.026A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 removed outlier: 4.194A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 967 removed outlier: 3.744A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.084A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.787A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 3.879A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 4.121A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1184 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1220 through 1230 removed outlier: 3.829A pdb=" N PHE B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.797A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1236 through 1240' Processing helix chain 'B' and resid 1241 through 1259 removed outlier: 3.585A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1273 Processing helix chain 'B' and resid 1282 through 1294 Processing helix chain 'B' and resid 1307 through 1310 Processing helix chain 'E' and resid 52 through 57 Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.641A pdb=" N LEU E 296 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 310 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.146A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.556A pdb=" N THR E 405 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 407 " --> pdb=" O ASP E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'G' and resid 304 through 312 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.699A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 328 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.824A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 541 through 569 Processing sheet with id=AA1, first strand: chain 'D' and resid 244 through 245 Processing sheet with id=AA2, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.677A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.252A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.439A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'S' and resid 83 through 84 removed outlier: 6.931A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.025A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'A' and resid 233 through 238 removed outlier: 8.095A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 21 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TYR A 64 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR A 23 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 66 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 756 through 757 removed outlier: 4.081A pdb=" N LYS B 756 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id=AB6, first strand: chain 'E' and resid 272 through 275 removed outlier: 4.115A pdb=" N CYS E 275 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS E 280 " --> pdb=" O CYS E 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AB8, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AB9, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.632A pdb=" N TYR E 505 " --> pdb=" O ILE E 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.514A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 992 hydrogen bonds defined for protein. 2904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 15.54 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7634 1.34 - 1.47: 8286 1.47 - 1.59: 11407 1.59 - 1.72: 636 1.72 - 1.85: 142 Bond restraints: 28105 Sorted by residual: bond pdb=" C MET B 765 " pdb=" N PRO B 766 " ideal model delta sigma weight residual 1.334 1.377 -0.043 1.51e-02 4.39e+03 8.05e+00 bond pdb=" N VAL A 102 " pdb=" CA VAL A 102 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" C ASN B1004 " pdb=" N PRO B1005 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.36e-02 5.41e+03 6.82e+00 bond pdb=" N LYS A 103 " pdb=" CA LYS A 103 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.70e+00 bond pdb=" N ASN E 347 " pdb=" CA ASN E 347 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.45e-02 4.76e+03 5.50e+00 ... (remaining 28100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 38941 2.97 - 5.93: 273 5.93 - 8.90: 62 8.90 - 11.86: 15 11.86 - 14.83: 5 Bond angle restraints: 39296 Sorted by residual: angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.61 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" CB LYS B 962 " pdb=" CG LYS B 962 " pdb=" CD LYS B 962 " ideal model delta sigma weight residual 111.30 122.72 -11.42 2.30e+00 1.89e-01 2.47e+01 angle pdb=" CB MET S 90 " pdb=" CG MET S 90 " pdb=" SD MET S 90 " ideal model delta sigma weight residual 112.70 127.53 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA GLN F 305 " pdb=" CB GLN F 305 " pdb=" CG GLN F 305 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CB MET O 90 " pdb=" CG MET O 90 " pdb=" SD MET O 90 " ideal model delta sigma weight residual 112.70 126.23 -13.53 3.00e+00 1.11e-01 2.03e+01 ... (remaining 39291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 14067 35.18 - 70.36: 1981 70.36 - 105.55: 51 105.55 - 140.73: 2 140.73 - 175.91: 1 Dihedral angle restraints: 16102 sinusoidal: 8750 harmonic: 7352 Sorted by residual: dihedral pdb=" CA LEU B1184 " pdb=" C LEU B1184 " pdb=" N ASP B1185 " pdb=" CA ASP B1185 " ideal model delta harmonic sigma weight residual 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA MET F 347 " pdb=" C MET F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA HIS E 302 " pdb=" C HIS E 302 " pdb=" N CYS E 303 " pdb=" CA CYS E 303 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 16099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3613 0.052 - 0.103: 606 0.103 - 0.155: 111 0.155 - 0.207: 11 0.207 - 0.259: 2 Chirality restraints: 4343 Sorted by residual: chirality pdb=" CB ILE F 105 " pdb=" CA ILE F 105 " pdb=" CG1 ILE F 105 " pdb=" CG2 ILE F 105 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL B 777 " pdb=" CA VAL B 777 " pdb=" CG1 VAL B 777 " pdb=" CG2 VAL B 777 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU F 338 " pdb=" CB LEU F 338 " pdb=" CD1 LEU F 338 " pdb=" CD2 LEU F 338 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4340 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 321 " -0.088 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO D 322 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 292 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO E 293 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 293 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 293 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.015 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP B 775 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.002 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 345 2.62 - 3.19: 21665 3.19 - 3.76: 48180 3.76 - 4.33: 62272 4.33 - 4.90: 94710 Nonbonded interactions: 227172 Sorted by model distance: nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.044 2.104 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.139 3.880 nonbonded pdb=" O ASN B1165 " pdb=" OG1 THR B1169 " model vdw 2.221 3.040 nonbonded pdb=" O LYS D 243 " pdb=" OG1 THR D 390 " model vdw 2.234 3.040 nonbonded pdb=" O ILE E 395 " pdb=" NZ LYS E 397 " model vdw 2.260 3.120 ... (remaining 227167 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' } 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: 10.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.160 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 74.930 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28107 Z= 0.171 Angle : 0.749 14.828 39298 Z= 0.400 Chirality : 0.040 0.259 4343 Planarity : 0.005 0.131 3879 Dihedral : 24.457 175.912 11345 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.29 % Favored : 95.59 % Rotamer: Outliers : 0.54 % Allowed : 32.75 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 2450 helix: -0.12 (0.13), residues: 1323 sheet: 0.76 (0.67), residues: 81 loop : -1.75 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 775 HIS 0.017 0.001 HIS E 302 PHE 0.038 0.001 PHE E 326 TYR 0.032 0.001 TYR A 176 ARG 0.016 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.15766 ( 1340) hydrogen bonds : angle 5.53322 ( 3600) metal coordination : bond 0.00002 ( 1) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.88978 ( 2) covalent geometry : bond 0.00349 (28105) covalent geometry : angle 0.74939 (39296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 315 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 291 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7906 (mmtt) REVERT: D 350 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 256 MET cc_start: 0.5695 (tpp) cc_final: 0.5075 (pmt) REVERT: P 84 MET cc_start: 0.8088 (tpp) cc_final: 0.7885 (tpp) REVERT: Q 95 LYS cc_start: 0.7854 (ttmp) cc_final: 0.7254 (tptt) REVERT: U 74 LYS cc_start: 0.7341 (mppt) cc_final: 0.7077 (mppt) REVERT: V 60 ASN cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: B 726 TYR cc_start: 0.6199 (t80) cc_final: 0.5780 (t80) REVERT: B 757 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8121 (ttp80) REVERT: B 773 MET cc_start: 0.5049 (ppp) cc_final: 0.4287 (ppp) REVERT: B 813 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 1185 ASP cc_start: 0.8091 (t70) cc_final: 0.7787 (t0) REVERT: B 1288 LEU cc_start: 0.7932 (tm) cc_final: 0.7617 (tm) REVERT: E 282 PHE cc_start: 0.6906 (m-10) cc_final: 0.6197 (m-10) outliers start: 12 outliers final: 3 residues processed: 319 average time/residue: 1.1713 time to fit residues: 444.9554 Evaluate side-chains 291 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain B residue 785 HIS Chi-restraints excluded: chain E residue 540 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN D 389 ASN F 263 HIS F 305 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS O 93 GLN U 38 ASN ** V 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 516 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.126071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093213 restraints weight = 56163.437| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.28 r_work: 0.3222 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 28107 Z= 0.330 Angle : 0.718 11.216 39298 Z= 0.390 Chirality : 0.045 0.234 4343 Planarity : 0.005 0.083 3879 Dihedral : 26.963 179.357 6228 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.40 % Allowed : 25.19 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2450 helix: 0.30 (0.14), residues: 1365 sheet: 0.28 (0.60), residues: 89 loop : -1.50 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1151 HIS 0.013 0.002 HIS T 75 PHE 0.023 0.002 PHE A 215 TYR 0.037 0.002 TYR P 88 ARG 0.007 0.001 ARG O 42 Details of bonding type rmsd hydrogen bonds : bond 0.05045 ( 1340) hydrogen bonds : angle 4.10345 ( 3600) metal coordination : bond 0.00600 ( 1) SS BOND : bond 0.00729 ( 1) SS BOND : angle 2.54590 ( 2) covalent geometry : bond 0.00739 (28105) covalent geometry : angle 0.71792 (39296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 351 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: D 291 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8511 (mmtt) REVERT: D 350 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7740 (tm-30) REVERT: F 256 MET cc_start: 0.5638 (tpp) cc_final: 0.5010 (pmt) REVERT: F 296 MET cc_start: 0.4523 (mtm) cc_final: 0.4222 (mpp) REVERT: F 368 MET cc_start: 0.3903 (ttt) cc_final: 0.3665 (ppp) REVERT: O 115 LYS cc_start: 0.9078 (mmtp) cc_final: 0.8840 (mmtm) REVERT: Q 99 ARG cc_start: 0.8322 (mpt180) cc_final: 0.8021 (mmm160) REVERT: R 54 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8532 (mmpt) REVERT: R 76 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: R 105 LYS cc_start: 0.8527 (pttm) cc_final: 0.8217 (ptpp) REVERT: U 29 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8949 (ttm170) REVERT: V 40 LYS cc_start: 0.8850 (mttm) cc_final: 0.8646 (mtmt) REVERT: V 87 THR cc_start: 0.9177 (p) cc_final: 0.8870 (p) REVERT: V 90 GLU cc_start: 0.8719 (mp0) cc_final: 0.8108 (mp0) REVERT: V 102 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: A 118 GLU cc_start: 0.8599 (mp0) cc_final: 0.8386 (mp0) REVERT: A 202 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7880 (mtp-110) REVERT: A 240 ASP cc_start: 0.8696 (m-30) cc_final: 0.8459 (m-30) REVERT: A 306 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7585 (tmm) REVERT: A 325 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: B 813 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8604 (mt-10) REVERT: B 825 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8054 (mm) REVERT: B 868 ARG cc_start: 0.8330 (tpp80) cc_final: 0.7993 (mtt-85) REVERT: B 976 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: B 1185 ASP cc_start: 0.8353 (t70) cc_final: 0.8116 (t0) REVERT: B 1187 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7144 (mm) REVERT: B 1285 ILE cc_start: 0.8623 (mm) cc_final: 0.8386 (mp) REVERT: E 500 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7099 (pttt) REVERT: E 501 LYS cc_start: 0.6937 (mmtt) cc_final: 0.6647 (mmtm) REVERT: E 542 ILE cc_start: 0.8091 (mm) cc_final: 0.7735 (tt) REVERT: E 544 GLU cc_start: 0.8379 (mp0) cc_final: 0.7958 (mp0) outliers start: 120 outliers final: 34 residues processed: 432 average time/residue: 1.4248 time to fit residues: 710.3567 Evaluate side-chains 326 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 63 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN D 267 GLN D 275 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN F 305 GLN O 76 GLN O 108 ASN Q 38 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 GLN V 44 GLN V 60 ASN V 106 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.126030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093259 restraints weight = 56050.348| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.10 r_work: 0.3243 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28107 Z= 0.180 Angle : 0.589 11.119 39298 Z= 0.323 Chirality : 0.038 0.178 4343 Planarity : 0.004 0.073 3879 Dihedral : 26.945 176.732 6225 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.95 % Allowed : 26.09 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2450 helix: 0.84 (0.14), residues: 1354 sheet: -0.04 (0.61), residues: 84 loop : -1.36 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 PHE 0.021 0.001 PHE G 326 TYR 0.019 0.001 TYR A 176 ARG 0.011 0.001 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1340) hydrogen bonds : angle 3.78380 ( 3600) metal coordination : bond 0.00316 ( 1) SS BOND : bond 0.00766 ( 1) SS BOND : angle 2.50805 ( 2) covalent geometry : bond 0.00403 (28105) covalent geometry : angle 0.58840 (39296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 321 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7508 (mmm) cc_final: 0.6729 (mpt) REVERT: D 275 GLN cc_start: 0.7430 (mm110) cc_final: 0.7048 (mm-40) REVERT: D 291 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8525 (mmtt) REVERT: D 308 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7658 (mm-30) REVERT: D 350 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 364 VAL cc_start: 0.8836 (m) cc_final: 0.8290 (p) REVERT: F 256 MET cc_start: 0.5675 (tpp) cc_final: 0.5092 (pmt) REVERT: O 115 LYS cc_start: 0.9075 (mmtp) cc_final: 0.8834 (mmtm) REVERT: Q 92 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8349 (mt-10) REVERT: Q 99 ARG cc_start: 0.8320 (mpt180) cc_final: 0.8058 (mmm160) REVERT: R 105 LYS cc_start: 0.8483 (pttm) cc_final: 0.8280 (ptpp) REVERT: S 42 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7933 (ptm-80) REVERT: S 59 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: T 35 ARG cc_start: 0.8317 (mtm110) cc_final: 0.8042 (mtm-85) REVERT: V 82 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8427 (mmtm) REVERT: V 90 GLU cc_start: 0.8679 (mp0) cc_final: 0.8456 (mp0) REVERT: V 102 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: A 60 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.5876 (ptpp) REVERT: A 67 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7717 (pptt) REVERT: A 118 GLU cc_start: 0.8587 (mp0) cc_final: 0.8330 (mp0) REVERT: A 211 TYR cc_start: 0.8152 (t80) cc_final: 0.7747 (t80) REVERT: A 325 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: A 373 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7766 (mtt) REVERT: B 825 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 868 ARG cc_start: 0.8392 (tpp80) cc_final: 0.7909 (mtt-85) REVERT: B 912 TRP cc_start: 0.8747 (m100) cc_final: 0.8413 (m100) REVERT: B 1185 ASP cc_start: 0.8254 (t70) cc_final: 0.8036 (t0) REVERT: B 1187 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7109 (mm) REVERT: B 1244 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8392 (mptp) REVERT: B 1285 ILE cc_start: 0.8668 (mm) cc_final: 0.8403 (mp) REVERT: E 500 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7091 (pttt) REVERT: E 501 LYS cc_start: 0.6808 (mmtt) cc_final: 0.6523 (mmtm) REVERT: E 523 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7576 (pt) REVERT: E 542 ILE cc_start: 0.8244 (mm) cc_final: 0.7923 (tt) REVERT: E 554 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8417 (tmtm) REVERT: E 559 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7137 (ptmt) REVERT: G 552 PHE cc_start: 0.8092 (t80) cc_final: 0.7820 (m-10) outliers start: 110 outliers final: 32 residues processed: 392 average time/residue: 1.4164 time to fit residues: 641.2951 Evaluate side-chains 328 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 192 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 269 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 521 GLN ** 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 = 0.3996 r_free = 0.3996 target = 0.124073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089166 restraints weight = 56564.533| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.98 r_work: 0.3231 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28107 Z= 0.191 Angle : 0.594 10.161 39298 Z= 0.326 Chirality : 0.038 0.177 4343 Planarity : 0.004 0.066 3879 Dihedral : 26.917 177.388 6225 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.14 % Allowed : 26.63 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2450 helix: 1.03 (0.14), residues: 1359 sheet: -0.25 (0.60), residues: 86 loop : -1.28 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 PHE 0.014 0.001 PHE B1147 TYR 0.021 0.001 TYR A 58 ARG 0.009 0.000 ARG R 30 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1340) hydrogen bonds : angle 3.70768 ( 3600) metal coordination : bond 0.00344 ( 1) SS BOND : bond 0.00614 ( 1) SS BOND : angle 0.75135 ( 2) covalent geometry : bond 0.00430 (28105) covalent geometry : angle 0.59395 (39296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 315 time to evaluate : 2.468 Fit side-chains revert: symmetry clash REVERT: D 22 MET cc_start: 0.7666 (mmm) cc_final: 0.6889 (mpt) REVERT: D 103 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6760 (pp20) REVERT: D 291 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8686 (mmtt) REVERT: D 308 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7916 (mm-30) REVERT: D 350 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7703 (tm-30) REVERT: D 364 VAL cc_start: 0.8818 (m) cc_final: 0.8520 (t) REVERT: F 256 MET cc_start: 0.5735 (tpp) cc_final: 0.5161 (pmt) REVERT: F 317 GLN cc_start: 0.4860 (OUTLIER) cc_final: 0.4604 (pm20) REVERT: F 347 MET cc_start: 0.1897 (pp-130) cc_final: 0.1480 (pp-130) REVERT: F 357 LYS cc_start: 0.8253 (tptm) cc_final: 0.7550 (mmtm) REVERT: O 115 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8909 (mmtm) REVERT: Q 99 ARG cc_start: 0.8525 (mpt180) cc_final: 0.8231 (mmm160) REVERT: S 59 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8331 (pm20) REVERT: U 29 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.9102 (ttm170) REVERT: V 82 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8530 (mmtm) REVERT: V 102 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: A 60 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6247 (ptpp) REVERT: A 67 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7853 (pptt) REVERT: A 118 GLU cc_start: 0.8700 (mp0) cc_final: 0.8477 (mp0) REVERT: A 160 PHE cc_start: 0.8604 (m-80) cc_final: 0.8398 (m-80) REVERT: A 306 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.7799 (tmm) REVERT: A 325 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 373 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7942 (mtt) REVERT: B 699 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8193 (mm) REVERT: B 813 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8550 (mp0) REVERT: B 825 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8132 (mm) REVERT: B 860 MET cc_start: 0.6594 (mpp) cc_final: 0.5907 (mpt) REVERT: B 868 ARG cc_start: 0.8350 (tpp80) cc_final: 0.7891 (mtt-85) REVERT: B 1187 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7080 (mm) REVERT: B 1244 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8562 (mptp) REVERT: B 1285 ILE cc_start: 0.8727 (mm) cc_final: 0.8469 (mp) REVERT: E 272 PHE cc_start: 0.7015 (m-10) cc_final: 0.6807 (m-80) REVERT: E 500 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7072 (pttt) REVERT: E 501 LYS cc_start: 0.6925 (mmtt) cc_final: 0.6464 (mptp) REVERT: E 554 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8561 (tmtm) REVERT: E 559 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7164 (ptmt) outliers start: 92 outliers final: 37 residues processed: 374 average time/residue: 1.5115 time to fit residues: 649.1111 Evaluate side-chains 332 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5914 > 50: distance: 92 - 98: 5.949 distance: 98 - 99: 8.656 distance: 99 - 100: 7.137 distance: 99 - 102: 8.091 distance: 100 - 101: 18.080 distance: 100 - 109: 6.860 distance: 102 - 103: 10.002 distance: 103 - 105: 7.509 distance: 104 - 106: 6.011 distance: 105 - 107: 5.746 distance: 106 - 108: 5.363 distance: 107 - 108: 8.028 distance: 109 - 110: 6.838 distance: 110 - 111: 15.960 distance: 110 - 113: 11.377 distance: 111 - 112: 8.391 distance: 111 - 117: 12.978 distance: 113 - 114: 9.912 distance: 114 - 115: 18.683 distance: 114 - 116: 5.454 distance: 117 - 118: 18.886 distance: 118 - 119: 8.064 distance: 118 - 121: 15.994 distance: 119 - 120: 25.228 distance: 119 - 123: 24.144 distance: 121 - 122: 30.436 distance: 123 - 124: 13.790 distance: 124 - 125: 6.111 distance: 124 - 127: 21.902 distance: 125 - 126: 28.930 distance: 125 - 131: 19.138 distance: 127 - 128: 28.223 distance: 128 - 129: 22.664 distance: 128 - 130: 35.870 distance: 131 - 132: 16.748 distance: 132 - 133: 11.224 distance: 132 - 135: 18.039 distance: 133 - 134: 32.385 distance: 133 - 139: 22.760 distance: 135 - 136: 39.609 distance: 136 - 137: 9.831 distance: 136 - 138: 14.946 distance: 139 - 140: 14.299 distance: 139 - 145: 15.895 distance: 140 - 141: 8.236 distance: 140 - 143: 4.335 distance: 141 - 142: 29.257 distance: 141 - 146: 12.961 distance: 143 - 144: 22.897 distance: 144 - 145: 23.708 distance: 146 - 147: 4.861 distance: 146 - 152: 14.736 distance: 147 - 148: 29.648 distance: 147 - 150: 17.765 distance: 148 - 149: 20.246 distance: 148 - 153: 22.488 distance: 150 - 151: 11.540 distance: 151 - 152: 12.863 distance: 153 - 154: 14.453 distance: 154 - 155: 12.863 distance: 154 - 157: 19.858 distance: 155 - 156: 28.727 distance: 155 - 161: 20.614 distance: 157 - 158: 34.689 distance: 157 - 159: 28.247 distance: 158 - 160: 34.703 distance: 161 - 162: 8.212 distance: 162 - 163: 26.094 distance: 162 - 165: 11.231 distance: 163 - 164: 10.957 distance: 163 - 169: 23.190 distance: 164 - 183: 27.721 distance: 165 - 166: 10.026 distance: 166 - 167: 41.093 distance: 166 - 168: 12.656 distance: 169 - 170: 14.615 distance: 169 - 175: 14.889 distance: 170 - 171: 30.222 distance: 170 - 173: 19.523 distance: 171 - 172: 5.293 distance: 171 - 176: 13.222 distance: 173 - 174: 17.779 distance: 174 - 175: 37.686