Starting phenix.real_space_refine on Mon Aug 10 02:53:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tax_55758/08_2026/9tax_55758.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tax_55758/08_2026/9tax_55758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tax_55758/08_2026/9tax_55758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tax_55758/08_2026/9tax_55758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tax_55758/08_2026/9tax_55758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tax_55758/08_2026/9tax_55758.map" } resolution = 4.5 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= 0.000 sd= 0.001 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 398 5.49 5 S 147 5.16 5 C 24330 2.51 5 N 7088 2.21 5 O 8239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40202 Number of models: 1 Model: "" Number of chains: 27 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1678 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain breaks: 1 Chain: "I" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5051 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 21, 'TRANS': 600} Chain breaks: 5 Chain: "K" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1936 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 2 Chain: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "L" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2506 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 Chain: "N" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2631 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 2 Chain: "O" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1681 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 201} Chain breaks: 2 Chain: "P" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1819 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Chain: "Q" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1530 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "U" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1377 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Chain: "T" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "W" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "S" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "V" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 4078 Classifications: {'DNA': 199} Link IDs: {'rna3p': 198} Chain: "Y" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 4081 Classifications: {'DNA': 199} Link IDs: {'rna3p': 198} Chain: "a" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 178 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "b" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 476 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 2 Chain: "c" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "d" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "e" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "f" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "g" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain breaks: 1 Chain: "h" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "i" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "j" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Time building chain proxies: 8.17, per 1000 atoms: 0.20 Number of scatterers: 40202 At special positions: 0 Unit cell: (189.744, 192.96, 237.984, 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 147 16.00 P 398 15.00 O 8239 8.00 N 7088 7.00 C 24330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7628 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 28 sheets defined 67.5% alpha, 8.5% beta 192 base pairs and 334 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'H' and resid 35 through 65 Processing helix chain 'H' and resid 76 through 115 Processing helix chain 'H' and resid 115 through 120 Processing helix chain 'H' and resid 124 through 188 removed outlier: 3.648A pdb=" N ASP H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 224 removed outlier: 4.449A pdb=" N ILE H 197 " --> pdb=" O GLU H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 229 Processing helix chain 'H' and resid 230 through 241 removed outlier: 4.379A pdb=" N ILE H 236 " --> pdb=" O ALA H 232 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 Processing helix chain 'I' and resid 82 through 102 removed outlier: 3.708A pdb=" N LYS I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 119 Processing helix chain 'I' and resid 122 through 132 Processing helix chain 'I' and resid 140 through 154 removed outlier: 3.617A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 184 through 191 removed outlier: 3.844A pdb=" N SER I 191 " --> pdb=" O PHE I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 194 No H-bonds generated for 'chain 'I' and resid 192 through 194' Processing helix chain 'I' and resid 197 through 209 Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 232 through 246 Processing helix chain 'I' and resid 269 through 282 Processing helix chain 'I' and resid 328 through 333 Processing helix chain 'I' and resid 340 through 344 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 362 through 368 removed outlier: 4.066A pdb=" N LEU I 367 " --> pdb=" O GLY I 364 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN I 368 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 376 Processing helix chain 'I' and resid 377 through 379 No H-bonds generated for 'chain 'I' and resid 377 through 379' Processing helix chain 'I' and resid 381 through 400 Processing helix chain 'I' and resid 402 through 407 removed outlier: 4.707A pdb=" N ASN I 407 " --> pdb=" O TYR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 410 No H-bonds generated for 'chain 'I' and resid 408 through 410' Processing helix chain 'I' and resid 411 through 427 Processing helix chain 'I' and resid 428 through 430 No H-bonds generated for 'chain 'I' and resid 428 through 430' Processing helix chain 'I' and resid 432 through 443 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.550A pdb=" N VAL I 459 " --> pdb=" O PHE I 455 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TRP I 461 " --> pdb=" O GLN I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 474 Proline residue: I 472 - end of helix Processing helix chain 'I' and resid 474 through 483 Processing helix chain 'I' and resid 486 through 514 Processing helix chain 'I' and resid 525 through 551 Processing helix chain 'I' and resid 554 through 570 removed outlier: 3.707A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP I 570 " --> pdb=" O GLU I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 576 Processing helix chain 'I' and resid 584 through 593 Processing helix chain 'I' and resid 596 through 625 removed outlier: 4.281A pdb=" N VAL I 623 " --> pdb=" O LYS I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 653 Processing helix chain 'I' and resid 664 through 672 removed outlier: 3.850A pdb=" N LEU I 668 " --> pdb=" O ASP I 664 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU I 669 " --> pdb=" O PRO I 665 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS I 670 " --> pdb=" O GLU I 666 " (cutoff:3.500A) Processing helix chain 'I' and resid 685 through 687 No H-bonds generated for 'chain 'I' and resid 685 through 687' Processing helix chain 'I' and resid 688 through 697 Processing helix chain 'I' and resid 719 through 726 Processing helix chain 'I' and resid 728 through 740 Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 54 through 76 Processing helix chain 'K' and resid 85 through 149 Processing helix chain 'K' and resid 155 through 188 removed outlier: 3.533A pdb=" N PHE K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 226 removed outlier: 3.538A pdb=" N MET K 215 " --> pdb=" O THR K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 removed outlier: 3.585A pdb=" N VAL K 243 " --> pdb=" O TRP K 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 38 removed outlier: 4.169A pdb=" N GLU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 86 removed outlier: 3.776A pdb=" N ARG M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 88 No H-bonds generated for 'chain 'M' and resid 87 through 88' Processing helix chain 'M' and resid 89 through 94 Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'M' and resid 113 through 125 removed outlier: 3.882A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 removed outlier: 4.529A pdb=" N THR M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'L' and resid 27 through 37 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 84 through 86 No H-bonds generated for 'chain 'L' and resid 84 through 86' Processing helix chain 'L' and resid 87 through 104 Processing helix chain 'L' and resid 167 through 173 removed outlier: 3.955A pdb=" N THR L 173 " --> pdb=" O SER L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 Processing helix chain 'L' and resid 214 through 228 Processing helix chain 'L' and resid 257 through 269 Processing helix chain 'L' and resid 276 through 296 Processing helix chain 'L' and resid 298 through 302 Processing helix chain 'L' and resid 324 through 326 No H-bonds generated for 'chain 'L' and resid 324 through 326' Processing helix chain 'L' and resid 327 through 344 Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.670A pdb=" N LYS N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 39 removed outlier: 4.047A pdb=" N VAL N 39 " --> pdb=" O GLN N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 62 through 78 Processing helix chain 'N' and resid 100 through 116 Processing helix chain 'N' and resid 166 through 170 removed outlier: 4.021A pdb=" N ARG N 169 " --> pdb=" O SER N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 304 through 313 removed outlier: 4.457A pdb=" N ALA N 310 " --> pdb=" O LEU N 306 " (cutoff:3.500A) Proline residue: N 311 - end of helix Processing helix chain 'N' and resid 320 through 325 Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'O' and resid 17 through 27 Processing helix chain 'O' and resid 90 through 109 Processing helix chain 'O' and resid 160 through 169 Processing helix chain 'O' and resid 172 through 201 Processing helix chain 'O' and resid 202 through 204 No H-bonds generated for 'chain 'O' and resid 202 through 204' Processing helix chain 'O' and resid 261 through 276 removed outlier: 4.113A pdb=" N GLU O 265 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 289 Processing helix chain 'P' and resid 54 through 74 Processing helix chain 'P' and resid 147 through 161 removed outlier: 3.786A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 191 removed outlier: 3.590A pdb=" N PHE P 166 " --> pdb=" O ASP P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 250 Processing helix chain 'P' and resid 254 through 256 No H-bonds generated for 'chain 'P' and resid 254 through 256' Processing helix chain 'P' and resid 257 through 270 removed outlier: 4.443A pdb=" N ARG P 263 " --> pdb=" O PRO P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 283 Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 102 through 122 Processing helix chain 'Q' and resid 133 through 199 removed outlier: 4.171A pdb=" N SER Q 138 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER Q 139 " --> pdb=" O THR Q 135 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN Q 199 " --> pdb=" O GLU Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 220 Processing helix chain 'Q' and resid 223 through 231 Processing helix chain 'Q' and resid 234 through 248 Processing helix chain 'Q' and resid 248 through 268 removed outlier: 3.659A pdb=" N LYS Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 269 removed outlier: 4.048A pdb=" N GLU U 257 " --> pdb=" O ILE U 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 375 Proline residue: U 332 - end of helix Processing helix chain 'U' and resid 383 through 385 No H-bonds generated for 'chain 'U' and resid 383 through 385' Processing helix chain 'U' and resid 386 through 399 removed outlier: 4.397A pdb=" N THR U 396 " --> pdb=" O PHE U 392 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU U 397 " --> pdb=" O LYS U 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 417 Processing helix chain 'R' and resid 85 through 96 Processing helix chain 'R' and resid 96 through 107 Processing helix chain 'R' and resid 107 through 112 removed outlier: 3.538A pdb=" N GLN R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 4.296A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 149 Processing helix chain 'R' and resid 168 through 177 Processing helix chain 'T' and resid 454 through 472 removed outlier: 3.975A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS T 472 " --> pdb=" O SER T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 477 through 506 Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.615A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 540 through 548 removed outlier: 3.792A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 Processing helix chain 'W' and resid 38 through 65 Processing helix chain 'W' and resid 71 through 87 removed outlier: 3.531A pdb=" N VAL W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 38 Processing helix chain 'S' and resid 43 through 72 Processing helix chain 'S' and resid 78 through 86 removed outlier: 3.656A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 120 Processing helix chain 'X' and resid 4 through 15 removed outlier: 3.620A pdb=" N HIS X 15 " --> pdb=" O LEU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 53 Processing helix chain 'X' and resid 59 through 65 Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'b' and resid 261 through 272 Processing helix chain 'b' and resid 273 through 275 No H-bonds generated for 'chain 'b' and resid 273 through 275' Processing helix chain 'b' and resid 297 through 303 removed outlier: 3.809A pdb=" N GLU b 302 " --> pdb=" O LEU b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 519 through 521 No H-bonds generated for 'chain 'b' and resid 519 through 521' Processing helix chain 'c' and resid 46 through 57 Processing helix chain 'c' and resid 63 through 77 removed outlier: 3.630A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS c 77 " --> pdb=" O GLU c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 116 Processing helix chain 'c' and resid 122 through 134 Processing helix chain 'd' and resid 30 through 41 Processing helix chain 'd' and resid 49 through 76 removed outlier: 3.825A pdb=" N GLU d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 93 removed outlier: 3.553A pdb=" N GLN d 93 " --> pdb=" O ALA d 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 22 Processing helix chain 'e' and resid 27 through 37 Processing helix chain 'e' and resid 45 through 73 removed outlier: 3.889A pdb=" N VAL e 49 " --> pdb=" O ALA e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 89 removed outlier: 3.523A pdb=" N LEU e 83 " --> pdb=" O ILE e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 97 Processing helix chain 'e' and resid 112 through 116 Processing helix chain 'f' and resid 37 through 49 removed outlier: 3.852A pdb=" N LEU f 45 " --> pdb=" O VAL f 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN f 47 " --> pdb=" O LYS f 43 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL f 48 " --> pdb=" O VAL f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 84 Processing helix chain 'f' and resid 90 through 102 Processing helix chain 'f' and resid 104 through 124 removed outlier: 3.553A pdb=" N SER f 123 " --> pdb=" O THR f 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 57 Processing helix chain 'g' and resid 63 through 80 removed outlier: 3.514A pdb=" N VAL g 76 " --> pdb=" O ARG g 72 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS g 77 " --> pdb=" O GLU g 73 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE g 78 " --> pdb=" O ILE g 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 116 Processing helix chain 'g' and resid 122 through 134 Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 30 through 41 removed outlier: 3.610A pdb=" N GLY h 41 " --> pdb=" O LEU h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 76 removed outlier: 3.848A pdb=" N GLU h 53 " --> pdb=" O LEU h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 92 Processing helix chain 'i' and resid 27 through 37 Processing helix chain 'i' and resid 45 through 73 removed outlier: 3.785A pdb=" N VAL i 49 " --> pdb=" O ALA i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 89 Processing helix chain 'i' and resid 90 through 97 Processing helix chain 'i' and resid 112 through 116 Processing helix chain 'j' and resid 37 through 47 removed outlier: 3.689A pdb=" N LEU j 45 " --> pdb=" O VAL j 41 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN j 47 " --> pdb=" O LYS j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 84 removed outlier: 3.597A pdb=" N ASN j 84 " --> pdb=" O LEU j 80 " (cutoff:3.500A) Processing helix chain 'j' and resid 90 through 102 Processing helix chain 'j' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'I' and resid 250 through 251 Processing sheet with id=AA2, first strand: chain 'K' and resid 231 through 233 Processing sheet with id=AA3, first strand: chain 'M' and resid 128 through 130 removed outlier: 6.311A pdb=" N ILE M 66 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU M 100 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE M 68 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR M 102 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL M 70 " --> pdb=" O THR M 102 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LEU M 65 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR M 17 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA5, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.750A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.750A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP L 158 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER L 143 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL L 156 " --> pdb=" O SER L 143 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG L 306 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER L 308 " --> pdb=" O GLU L 238 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU L 250 " --> pdb=" O VAL L 243 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR N 273 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA8, first strand: chain 'N' and resid 119 through 126 removed outlier: 5.390A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP N 83 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU N 193 " --> pdb=" O TRP N 83 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL N 85 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN N 187 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 118 removed outlier: 4.306A pdb=" N VAL O 122 " --> pdb=" O LEU O 142 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE O 130 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU O 134 " --> pdb=" O PHE O 130 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE O 139 " --> pdb=" O HIS O 153 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS O 153 " --> pdb=" O PHE O 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP O 141 " --> pdb=" O HIS O 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 210 through 211 Processing sheet with id=AB2, first strand: chain 'P' and resid 76 through 87 removed outlier: 4.611A pdb=" N ILE P 78 " --> pdb=" O ASN P 110 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN P 110 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN P 80 " --> pdb=" O SER P 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG P 99 " --> pdb=" O GLN P 126 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR P 115 " --> pdb=" O MET P 142 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N MET P 142 " --> pdb=" O THR P 115 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN P 117 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE P 140 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU P 119 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU P 138 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 195 through 196 removed outlier: 4.830A pdb=" N SER P 210 " --> pdb=" O PHE P 216 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE P 216 " --> pdb=" O SER P 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'T' and resid 550 through 552 Processing sheet with id=AB6, first strand: chain 'S' and resid 41 through 42 removed outlier: 6.866A pdb=" N GLN S 41 " --> pdb=" O VAL X 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'S' and resid 76 through 77 Processing sheet with id=AB8, first strand: chain 'a' and resid 516 through 517 Processing sheet with id=AB9, first strand: chain 'b' and resid 516 through 517 Processing sheet with id=AC1, first strand: chain 'c' and resid 85 through 86 removed outlier: 6.122A pdb=" N ASN c 85 " --> pdb=" O VAL d 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'c' and resid 120 through 121 Processing sheet with id=AC3, first strand: chain 'd' and resid 96 through 98 removed outlier: 6.432A pdb=" N THR d 96 " --> pdb=" O THR i 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'e' and resid 42 through 43 removed outlier: 7.196A pdb=" N ARG e 42 " --> pdb=" O ILE f 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'e' and resid 77 through 78 Processing sheet with id=AC6, first strand: chain 'e' and resid 100 through 102 removed outlier: 3.656A pdb=" N THR e 101 " --> pdb=" O THR h 96 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR h 98 " --> pdb=" O THR e 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'g' and resid 85 through 86 removed outlier: 6.868A pdb=" N ASN g 85 " --> pdb=" O VAL h 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'g' and resid 120 through 121 Processing sheet with id=AC9, first strand: chain 'i' and resid 42 through 43 removed outlier: 7.198A pdb=" N ARG i 42 " --> pdb=" O ILE j 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'i' and resid 77 through 78 2136 hydrogen bonds defined for protein. 6288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 478 hydrogen bonds 956 hydrogen bond angles 0 basepair planarities 192 basepair parallelities 334 stacking parallelities Total time for adding SS restraints: 11.65 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10417 1.33 - 1.45: 9629 1.45 - 1.58: 20673 1.58 - 1.70: 794 1.70 - 1.82: 230 Bond restraints: 41743 Sorted by residual: bond pdb=" C3' DT Y-192 " pdb=" C2' DT Y-192 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C THR N 158 " pdb=" N PRO N 159 " ideal model delta sigma weight residual 1.331 1.304 0.027 7.90e-03 1.60e+04 1.18e+01 bond pdb=" C3' DG Y-224 " pdb=" C2' DG Y-224 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DA V 192 " pdb=" C2' DA V 192 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG Y-163 " pdb=" C2' DG Y-163 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 41738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 56854 2.26 - 4.52: 1052 4.52 - 6.78: 70 6.78 - 9.04: 15 9.04 - 11.31: 2 Bond angle restraints: 57993 Sorted by residual: angle pdb=" O4' DG V 155 " pdb=" C4' DG V 155 " pdb=" C3' DG V 155 " ideal model delta sigma weight residual 106.00 102.14 3.86 6.00e-01 2.78e+00 4.14e+01 angle pdb=" C CYS I 322 " pdb=" CA CYS I 322 " pdb=" CB CYS I 322 " ideal model delta sigma weight residual 117.23 110.12 7.11 1.36e+00 5.41e-01 2.73e+01 angle pdb=" N3 DT Y-190 " pdb=" C4 DT Y-190 " pdb=" O4 DT Y-190 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" C ILE I 134 " pdb=" N PRO I 135 " pdb=" CA PRO I 135 " ideal model delta sigma weight residual 119.84 125.49 -5.65 1.25e+00 6.40e-01 2.04e+01 angle pdb=" N3 DT V 313 " pdb=" C4 DT V 313 " pdb=" O4 DT V 313 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 57988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 22417 35.49 - 70.98: 1985 70.98 - 106.47: 39 106.47 - 141.96: 1 141.96 - 177.44: 4 Dihedral angle restraints: 24446 sinusoidal: 12789 harmonic: 11657 Sorted by residual: dihedral pdb=" CA TYR O 168 " pdb=" C TYR O 168 " pdb=" N LEU O 169 " pdb=" CA LEU O 169 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TRP K 239 " pdb=" C TRP K 239 " pdb=" N PRO K 240 " pdb=" CA PRO K 240 " ideal model delta harmonic sigma weight residual -180.00 -154.99 -25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LEU I 449 " pdb=" C LEU I 449 " pdb=" N CYS I 450 " pdb=" CA CYS I 450 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 24443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5643 0.060 - 0.120: 896 0.120 - 0.180: 56 0.180 - 0.240: 5 0.240 - 0.300: 3 Chirality restraints: 6603 Sorted by residual: chirality pdb=" CB ILE j 94 " pdb=" CA ILE j 94 " pdb=" CG1 ILE j 94 " pdb=" CG2 ILE j 94 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE f 94 " pdb=" CA ILE f 94 " pdb=" CG1 ILE f 94 " pdb=" CG2 ILE f 94 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB ILE N 71 " pdb=" CA ILE N 71 " pdb=" CG1 ILE N 71 " pdb=" CG2 ILE N 71 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 6600 not shown) Planarity restraints: 5925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 132 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.31e+00 pdb=" CG TRP N 132 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP N 132 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP N 132 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP N 132 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP N 132 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP N 132 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 132 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 132 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP N 132 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 176 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C PHE O 176 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE O 176 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU O 177 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 246 " -0.037 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO L 247 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 247 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 247 " -0.031 5.00e-02 4.00e+02 ... (remaining 5922 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 12688 2.86 - 3.37: 43488 3.37 - 3.88: 78029 3.88 - 4.39: 88857 4.39 - 4.90: 132095 Nonbonded interactions: 355157 Sorted by model distance: nonbonded pdb=" O CYS T 495 " pdb=" OE1 GLU T 499 " model vdw 2.347 3.040 nonbonded pdb=" O VAL c 103 " pdb=" OE1 GLU c 107 " model vdw 2.349 3.040 nonbonded pdb=" O ASN H 87 " pdb=" OE1 GLU H 91 " model vdw 2.354 3.040 nonbonded pdb=" O GLN H 52 " pdb=" OE1 GLU H 56 " model vdw 2.359 3.040 nonbonded pdb=" O LEU K 59 " pdb=" OE1 GLN K 63 " model vdw 2.407 3.040 ... (remaining 355152 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 'c' and (resid 42 through 87 or resid 89 through 140)) selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } ncs_group { reference = chain 'e' selection = chain 'i' } ncs_group { reference = (chain 'f' and resid 31 through 124) selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.270 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 43.100 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.200 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.005 0.056 41743 Z= 0.381 Angle : 0.723 11.306 57993 Z= 0.531 Chirality : 0.043 0.300 6603 Planarity : 0.004 0.055 5925 Dihedral : 20.474 177.444 16818 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.08 (0.13), residues: 3874 helix: 1.32 (0.10), residues: 2472 sheet: -0.41 (0.30), residues: 267 loop : -0.18 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 57 TYR 0.022 0.002 TYR L 207 PHE 0.030 0.002 PHE b 262 TRP 0.043 0.002 TRP N 132 HIS 0.012 0.001 HIS I 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.38 (41743) covalent geometry : angle 0.72275 / 0.53 (57993) hydrogen bonds : bond 0.11102 / 7.03 ( 2592) hydrogen bonds : angle 5.79222 / 4.13 ( 7244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.8974 (mmp) cc_final: 0.8522 (mmm) REVERT: H 189 MET cc_start: 0.9090 (mtm) cc_final: 0.8690 (mtm) REVERT: H 247 MET cc_start: 0.5590 (tmm) cc_final: 0.4680 (ppp) REVERT: I 229 MET cc_start: 0.9354 (mmp) cc_final: 0.9145 (mmm) REVERT: I 510 MET cc_start: 0.8445 (tpp) cc_final: 0.7872 (tpp) REVERT: I 514 MET cc_start: 0.7575 (ptt) cc_final: 0.6774 (ptt) REVERT: I 607 MET cc_start: 0.9083 (tpp) cc_final: 0.8357 (tpp) REVERT: K 97 PHE cc_start: 0.9264 (m-10) cc_final: 0.8980 (m-10) REVERT: K 136 MET cc_start: 0.9318 (tpt) cc_final: 0.9050 (tpp) REVERT: K 166 MET cc_start: 0.9227 (mmt) cc_final: 0.8828 (mmt) REVERT: K 215 MET cc_start: 0.9124 (ptp) cc_final: 0.8714 (ptp) REVERT: M 107 GLU cc_start: 0.9237 (pm20) cc_final: 0.9015 (mp0) REVERT: N 88 MET cc_start: 0.8615 (ttm) cc_final: 0.8378 (ttm) REVERT: P 206 MET cc_start: 0.6932 (tpt) cc_final: 0.6373 (tpt) REVERT: Q 88 MET cc_start: 0.9625 (ppp) cc_final: 0.9192 (ppp) REVERT: Q 200 MET cc_start: 0.8749 (ptt) cc_final: 0.8477 (ptt) REVERT: T 470 TYR cc_start: 0.9502 (m-80) cc_final: 0.9180 (m-80) REVERT: T 475 MET cc_start: 0.7529 (pmm) cc_final: 0.7267 (pmm) REVERT: T 478 LYS cc_start: 0.9704 (mmtt) cc_final: 0.9348 (tptp) REVERT: S 40 MET cc_start: 0.7747 (tpt) cc_final: 0.7008 (tpt) REVERT: S 55 PHE cc_start: 0.9500 (m-80) cc_final: 0.9185 (m-80) REVERT: S 67 MET cc_start: 0.9120 (ptp) cc_final: 0.8783 (ptp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2243 time to fit residues: 61.5554 Evaluate side-chains 133 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 726 GLN ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 453 GLN ** g 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 HIS ** 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 = 0.3983 r_free = 0.3983 target = 0.078273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.050640 restraints weight = 457000.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050173 restraints weight = 290258.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.050751 restraints weight = 202272.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050545 restraints weight = 149084.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050948 restraints weight = 138390.421| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 41743 Z= 0.240 Angle : 0.674 12.443 57993 Z= 0.374 Chirality : 0.042 0.298 6603 Planarity : 0.004 0.060 5925 Dihedral : 25.003 174.277 8661 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.09 (0.13), residues: 3874 helix: 1.38 (0.10), residues: 2497 sheet: -0.65 (0.29), residues: 270 loop : -0.30 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 223 TYR 0.021 0.002 TYR O 168 PHE 0.034 0.002 PHE U 281 TRP 0.025 0.002 TRP N 132 HIS 0.010 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.24 (41743) covalent geometry : angle 0.67419 / 0.37 (57993) hydrogen bonds : bond 0.05680 / 3.78 ( 2592) hydrogen bonds : angle 4.87667 / 3.49 ( 7244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9101 (mmp) cc_final: 0.8685 (mmm) REVERT: H 106 MET cc_start: 0.9554 (ptp) cc_final: 0.9332 (ptp) REVERT: H 189 MET cc_start: 0.9155 (mtm) cc_final: 0.8868 (mtm) REVERT: I 224 ASP cc_start: 0.9603 (m-30) cc_final: 0.9390 (m-30) REVERT: I 510 MET cc_start: 0.8596 (tpp) cc_final: 0.7933 (tpp) REVERT: I 514 MET cc_start: 0.7798 (ptt) cc_final: 0.6914 (ptt) REVERT: I 607 MET cc_start: 0.9213 (tpp) cc_final: 0.8507 (tpp) REVERT: K 97 PHE cc_start: 0.9302 (m-10) cc_final: 0.9028 (m-10) REVERT: K 136 MET cc_start: 0.9366 (tpt) cc_final: 0.8995 (tpp) REVERT: K 166 MET cc_start: 0.9235 (mmt) cc_final: 0.8882 (mmt) REVERT: M 31 LEU cc_start: 0.9440 (tt) cc_final: 0.8725 (tt) REVERT: M 35 MET cc_start: 0.9398 (mmm) cc_final: 0.8932 (mmp) REVERT: M 107 GLU cc_start: 0.9380 (pm20) cc_final: 0.9056 (mp0) REVERT: L 230 MET cc_start: 0.7031 (tpt) cc_final: 0.6062 (tpp) REVERT: N 88 MET cc_start: 0.8713 (ttm) cc_final: 0.8247 (mtt) REVERT: N 331 MET cc_start: 0.8947 (tpt) cc_final: 0.8479 (tpp) REVERT: Q 88 MET cc_start: 0.9623 (ppp) cc_final: 0.9184 (ppp) REVERT: Q 165 MET cc_start: 0.9524 (mtm) cc_final: 0.8875 (ttm) REVERT: Q 200 MET cc_start: 0.8863 (ptt) cc_final: 0.8437 (ptt) REVERT: U 320 MET cc_start: 0.9545 (ttt) cc_final: 0.9041 (tpp) REVERT: T 470 TYR cc_start: 0.9530 (m-80) cc_final: 0.9119 (m-10) REVERT: T 478 LYS cc_start: 0.9677 (mmtt) cc_final: 0.9332 (tptp) REVERT: T 482 MET cc_start: 0.9285 (tpp) cc_final: 0.8843 (tpt) REVERT: S 40 MET cc_start: 0.7787 (tpt) cc_final: 0.7146 (tpp) REVERT: S 55 PHE cc_start: 0.9516 (m-80) cc_final: 0.9202 (m-80) REVERT: d 84 MET cc_start: 0.4715 (ptt) cc_final: 0.4259 (ppp) outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.2138 time to fit residues: 56.9838 Evaluate side-chains 136 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 422 optimal weight: 7.9990 chunk 351 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 399 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 376 optimal weight: 10.0000 chunk 325 optimal weight: 50.0000 chunk 305 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 HIS ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN O 255 GLN ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 453 GLN S 41 GLN e 104 GLN f 67 ASN g 55 GLN ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 HIS ** 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 = 0.3978 r_free = 0.3978 target = 0.077963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.049989 restraints weight = 458173.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049998 restraints weight = 266818.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.050173 restraints weight = 207727.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050276 restraints weight = 152003.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050370 restraints weight = 146275.118| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 41743 Z= 0.235 Angle : 0.660 11.388 57993 Z= 0.367 Chirality : 0.042 0.292 6603 Planarity : 0.004 0.083 5925 Dihedral : 25.197 179.094 8661 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.06 (0.13), residues: 3874 helix: 1.40 (0.10), residues: 2487 sheet: -0.81 (0.29), residues: 277 loop : -0.35 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG P 104 TYR 0.019 0.002 TYR P 179 PHE 0.031 0.002 PHE U 281 TRP 0.034 0.002 TRP P 222 HIS 0.009 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.24 (41743) covalent geometry : angle 0.65967 / 0.37 (57993) hydrogen bonds : bond 0.05529 / 3.69 ( 2592) hydrogen bonds : angle 4.77071 / 3.42 ( 7244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9131 (mmp) cc_final: 0.8705 (mmm) REVERT: H 106 MET cc_start: 0.9586 (ptp) cc_final: 0.9379 (ptp) REVERT: H 189 MET cc_start: 0.9174 (mtm) cc_final: 0.8861 (mtm) REVERT: I 224 ASP cc_start: 0.9585 (m-30) cc_final: 0.9367 (m-30) REVERT: I 510 MET cc_start: 0.8638 (tpp) cc_final: 0.7926 (tpp) REVERT: I 514 MET cc_start: 0.7776 (ptt) cc_final: 0.6926 (ptt) REVERT: I 607 MET cc_start: 0.9496 (tpp) cc_final: 0.9293 (tpp) REVERT: K 97 PHE cc_start: 0.9328 (m-10) cc_final: 0.9055 (m-10) REVERT: K 136 MET cc_start: 0.9380 (tpt) cc_final: 0.9023 (tpp) REVERT: K 166 MET cc_start: 0.9232 (mmt) cc_final: 0.8816 (mmt) REVERT: M 31 LEU cc_start: 0.9474 (tt) cc_final: 0.8890 (tt) REVERT: M 35 MET cc_start: 0.9397 (mmm) cc_final: 0.9072 (mmm) REVERT: M 142 MET cc_start: 0.9469 (tpp) cc_final: 0.9238 (tpp) REVERT: L 230 MET cc_start: 0.7207 (tpt) cc_final: 0.6053 (tpp) REVERT: N 88 MET cc_start: 0.8715 (ttm) cc_final: 0.8312 (mtt) REVERT: Q 88 MET cc_start: 0.9688 (ppp) cc_final: 0.9305 (ppp) REVERT: Q 165 MET cc_start: 0.9519 (mtm) cc_final: 0.8909 (ttm) REVERT: Q 200 MET cc_start: 0.8957 (ptt) cc_final: 0.8451 (ptt) REVERT: U 320 MET cc_start: 0.9538 (ttt) cc_final: 0.9046 (tpp) REVERT: T 470 TYR cc_start: 0.9498 (m-80) cc_final: 0.9079 (m-10) REVERT: T 478 LYS cc_start: 0.9686 (mmtt) cc_final: 0.9348 (tptp) REVERT: S 40 MET cc_start: 0.8018 (tpt) cc_final: 0.7236 (tpp) REVERT: S 55 PHE cc_start: 0.9522 (m-80) cc_final: 0.9195 (m-80) REVERT: b 301 ASP cc_start: 0.7117 (t0) cc_final: 0.6898 (t0) REVERT: d 84 MET cc_start: 0.4767 (ptt) cc_final: 0.4300 (ppp) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.2225 time to fit residues: 58.9803 Evaluate side-chains 128 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 92 optimal weight: 3.9990 chunk 307 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 407 optimal weight: 30.0000 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 391 optimal weight: 50.0000 chunk 319 optimal weight: 50.0000 chunk 389 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 137 ASN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 ASN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 GLN N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 453 GLN ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.077974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049995 restraints weight = 457932.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.049518 restraints weight = 322347.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050149 restraints weight = 215410.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050076 restraints weight = 163952.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051114 restraints weight = 172355.516| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 41743 Z= 0.222 Angle : 0.643 11.772 57993 Z= 0.357 Chirality : 0.041 0.291 6603 Planarity : 0.004 0.059 5925 Dihedral : 25.313 179.915 8661 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.10 (0.13), residues: 3874 helix: 1.45 (0.10), residues: 2492 sheet: -0.84 (0.29), residues: 271 loop : -0.37 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 104 TYR 0.024 0.002 TYR I 389 PHE 0.030 0.002 PHE U 281 TRP 0.018 0.001 TRP P 222 HIS 0.016 0.001 HIS c 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (41743) covalent geometry : angle 0.64261 / 0.36 (57993) hydrogen bonds : bond 0.05306 / 3.54 ( 2592) hydrogen bonds : angle 4.66702 / 3.35 ( 7244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9114 (mmp) cc_final: 0.8689 (mmm) REVERT: H 106 MET cc_start: 0.9600 (ptp) cc_final: 0.9331 (ptp) REVERT: H 189 MET cc_start: 0.9165 (mtm) cc_final: 0.8883 (mtm) REVERT: I 224 ASP cc_start: 0.9591 (m-30) cc_final: 0.9381 (m-30) REVERT: I 510 MET cc_start: 0.8681 (tpp) cc_final: 0.7902 (tpp) REVERT: I 514 MET cc_start: 0.7797 (ptt) cc_final: 0.6943 (ptt) REVERT: K 97 PHE cc_start: 0.9364 (m-10) cc_final: 0.9063 (m-10) REVERT: K 136 MET cc_start: 0.9395 (tpt) cc_final: 0.9028 (tpp) REVERT: K 166 MET cc_start: 0.9217 (mmt) cc_final: 0.8795 (mmt) REVERT: M 31 LEU cc_start: 0.9497 (tt) cc_final: 0.8927 (tt) REVERT: M 35 MET cc_start: 0.9308 (mmm) cc_final: 0.8813 (mmm) REVERT: L 230 MET cc_start: 0.7160 (tpt) cc_final: 0.6048 (tpp) REVERT: N 88 MET cc_start: 0.8632 (ttm) cc_final: 0.8002 (mtt) REVERT: N 179 LEU cc_start: 0.9717 (tp) cc_final: 0.9487 (tp) REVERT: N 331 MET cc_start: 0.8821 (tpp) cc_final: 0.8367 (tpp) REVERT: Q 88 MET cc_start: 0.9723 (ppp) cc_final: 0.9289 (ppp) REVERT: Q 165 MET cc_start: 0.9501 (mtm) cc_final: 0.8885 (ttm) REVERT: Q 200 MET cc_start: 0.8862 (ptt) cc_final: 0.8227 (ptt) REVERT: U 320 MET cc_start: 0.9531 (ttt) cc_final: 0.9043 (tpp) REVERT: T 470 TYR cc_start: 0.9455 (m-80) cc_final: 0.9078 (m-80) REVERT: T 475 MET cc_start: 0.7836 (pmm) cc_final: 0.7572 (pmm) REVERT: T 478 LYS cc_start: 0.9702 (mmtt) cc_final: 0.9355 (tptp) REVERT: T 482 MET cc_start: 0.9317 (tpp) cc_final: 0.8847 (tpt) REVERT: S 40 MET cc_start: 0.7951 (tpt) cc_final: 0.7157 (tpp) REVERT: S 55 PHE cc_start: 0.9533 (m-80) cc_final: 0.9211 (m-80) REVERT: d 84 MET cc_start: 0.4814 (ptt) cc_final: 0.4342 (ppp) REVERT: j 47 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6409 (pt0) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.2132 time to fit residues: 54.9527 Evaluate side-chains 128 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 408 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 413 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 236 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 226 ASN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 HIS ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.079244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051535 restraints weight = 450441.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051236 restraints weight = 298619.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051919 restraints weight = 192836.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051462 restraints weight = 161039.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.051699 restraints weight = 147652.617| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41743 Z= 0.140 Angle : 0.597 11.015 57993 Z= 0.332 Chirality : 0.041 0.269 6603 Planarity : 0.004 0.055 5925 Dihedral : 25.296 178.268 8661 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.65 % Rotamer: Outliers : 0.06 % Allowed : 1.35 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.39 (0.14), residues: 3874 helix: 1.67 (0.10), residues: 2490 sheet: -0.65 (0.29), residues: 274 loop : -0.27 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 145 TYR 0.016 0.002 TYR i 50 PHE 0.037 0.002 PHE U 392 TRP 0.014 0.001 TRP L 265 HIS 0.008 0.001 HIS N 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (41743) covalent geometry : angle 0.59736 / 0.33 (57993) hydrogen bonds : bond 0.04641 / 3.11 ( 2592) hydrogen bonds : angle 4.42309 / 3.17 ( 7244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9040 (mmp) cc_final: 0.8562 (mmm) REVERT: H 189 MET cc_start: 0.9150 (mtm) cc_final: 0.8856 (mtm) REVERT: I 224 ASP cc_start: 0.9568 (m-30) cc_final: 0.9355 (m-30) REVERT: I 510 MET cc_start: 0.8668 (tpp) cc_final: 0.7772 (tpp) REVERT: I 514 MET cc_start: 0.7707 (ptt) cc_final: 0.6533 (ptt) REVERT: K 35 MET cc_start: 0.9153 (mmt) cc_final: 0.8435 (mmm) REVERT: K 62 MET cc_start: 0.9584 (mmp) cc_final: 0.9362 (mmp) REVERT: K 97 PHE cc_start: 0.9319 (m-10) cc_final: 0.9019 (m-10) REVERT: K 136 MET cc_start: 0.9359 (tpt) cc_final: 0.9050 (tpp) REVERT: K 166 MET cc_start: 0.9213 (mmt) cc_final: 0.8783 (mmt) REVERT: M 31 LEU cc_start: 0.9524 (tt) cc_final: 0.8955 (tt) REVERT: M 35 MET cc_start: 0.9244 (mmm) cc_final: 0.8772 (mmm) REVERT: M 107 GLU cc_start: 0.9387 (pm20) cc_final: 0.9091 (pm20) REVERT: L 230 MET cc_start: 0.6967 (tpt) cc_final: 0.5964 (tpp) REVERT: N 331 MET cc_start: 0.8842 (tpp) cc_final: 0.8440 (tpp) REVERT: Q 88 MET cc_start: 0.9586 (ppp) cc_final: 0.9158 (ppp) REVERT: Q 165 MET cc_start: 0.9505 (mtm) cc_final: 0.8916 (ttm) REVERT: Q 200 MET cc_start: 0.9027 (ptt) cc_final: 0.8474 (ptt) REVERT: U 320 MET cc_start: 0.9533 (ttt) cc_final: 0.9053 (tpp) REVERT: T 470 TYR cc_start: 0.9436 (m-80) cc_final: 0.9046 (m-10) REVERT: T 473 MET cc_start: 0.9315 (tpp) cc_final: 0.8616 (tpp) REVERT: S 40 MET cc_start: 0.7997 (tpt) cc_final: 0.7212 (tpp) REVERT: S 55 PHE cc_start: 0.9476 (m-80) cc_final: 0.9132 (m-80) REVERT: d 84 MET cc_start: 0.4904 (ptt) cc_final: 0.4462 (ppp) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.2153 time to fit residues: 61.4414 Evaluate side-chains 131 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 207 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 265 optimal weight: 0.0770 chunk 223 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 396 optimal weight: 50.0000 chunk 94 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 400 optimal weight: 30.0000 chunk 119 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 226 ASN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.078418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.051025 restraints weight = 457564.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.050694 restraints weight = 302474.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.051135 restraints weight = 203990.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.050880 restraints weight = 174429.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050868 restraints weight = 163196.184| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 41743 Z= 0.188 Angle : 0.620 11.478 57993 Z= 0.342 Chirality : 0.040 0.270 6603 Planarity : 0.004 0.055 5925 Dihedral : 25.327 177.268 8661 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 0.08 % Allowed : 1.66 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.40 (0.14), residues: 3874 helix: 1.69 (0.10), residues: 2484 sheet: -0.67 (0.29), residues: 274 loop : -0.29 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 104 TYR 0.015 0.002 TYR i 50 PHE 0.031 0.002 PHE R 86 TRP 0.014 0.001 TRP I 391 HIS 0.013 0.001 HIS c 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (41743) covalent geometry : angle 0.61985 / 0.34 (57993) hydrogen bonds : bond 0.04944 / 3.30 ( 2592) hydrogen bonds : angle 4.44692 / 3.19 ( 7244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9073 (mmp) cc_final: 0.8608 (mmm) REVERT: H 189 MET cc_start: 0.9130 (mtm) cc_final: 0.8811 (mtm) REVERT: I 224 ASP cc_start: 0.9549 (m-30) cc_final: 0.9349 (m-30) REVERT: I 510 MET cc_start: 0.8688 (tpp) cc_final: 0.7894 (tpp) REVERT: I 514 MET cc_start: 0.7776 (ptt) cc_final: 0.6959 (ptt) REVERT: K 35 MET cc_start: 0.9182 (mmt) cc_final: 0.8508 (mmm) REVERT: K 97 PHE cc_start: 0.9311 (m-10) cc_final: 0.9026 (m-10) REVERT: K 136 MET cc_start: 0.9361 (tpt) cc_final: 0.9013 (tpp) REVERT: K 166 MET cc_start: 0.9203 (mmt) cc_final: 0.8812 (mmt) REVERT: M 31 LEU cc_start: 0.9536 (tt) cc_final: 0.8951 (tt) REVERT: M 35 MET cc_start: 0.9214 (mmm) cc_final: 0.8811 (mmm) REVERT: M 107 GLU cc_start: 0.9394 (pm20) cc_final: 0.9151 (pm20) REVERT: L 230 MET cc_start: 0.7148 (tpt) cc_final: 0.5941 (tpp) REVERT: N 331 MET cc_start: 0.8737 (tpp) cc_final: 0.8295 (tpp) REVERT: P 113 MET cc_start: 0.9066 (mpp) cc_final: 0.8766 (mpp) REVERT: Q 88 MET cc_start: 0.9591 (ppp) cc_final: 0.9128 (ppp) REVERT: Q 165 MET cc_start: 0.9466 (mtm) cc_final: 0.8861 (ttm) REVERT: Q 200 MET cc_start: 0.9004 (ptt) cc_final: 0.8419 (ptt) REVERT: U 320 MET cc_start: 0.9511 (ttt) cc_final: 0.9035 (tpp) REVERT: T 470 TYR cc_start: 0.9411 (m-80) cc_final: 0.9058 (m-10) REVERT: T 475 MET cc_start: 0.7741 (pmm) cc_final: 0.7485 (pmm) REVERT: T 478 LYS cc_start: 0.9703 (mmtt) cc_final: 0.9328 (tptp) REVERT: S 40 MET cc_start: 0.8115 (tpt) cc_final: 0.7284 (tpp) REVERT: S 55 PHE cc_start: 0.9500 (m-80) cc_final: 0.9191 (m-80) REVERT: c 107 GLU cc_start: 0.9462 (OUTLIER) cc_final: 0.9255 (pp20) REVERT: d 84 MET cc_start: 0.4602 (ptt) cc_final: 0.4222 (ppp) outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 0.2167 time to fit residues: 60.8495 Evaluate side-chains 131 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 321 optimal weight: 50.0000 chunk 190 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 chunk 347 optimal weight: 20.0000 chunk 266 optimal weight: 40.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN L 232 HIS L 248 GLN N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 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 = 0.3972 r_free = 0.3972 target = 0.077718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.050161 restraints weight = 458999.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.049737 restraints weight = 304309.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.050442 restraints weight = 201257.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.049746 restraints weight = 171403.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.049836 restraints weight = 179055.665| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 41743 Z= 0.229 Angle : 0.662 11.264 57993 Z= 0.363 Chirality : 0.042 0.335 6603 Planarity : 0.004 0.058 5925 Dihedral : 25.423 179.608 8661 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 1.20 (0.13), residues: 3874 helix: 1.54 (0.10), residues: 2485 sheet: -0.77 (0.29), residues: 273 loop : -0.36 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 544 TYR 0.016 0.002 TYR i 50 PHE 0.031 0.002 PHE N 8 TRP 0.052 0.002 TRP K 239 HIS 0.010 0.002 HIS N 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.23 (41743) covalent geometry : angle 0.66208 / 0.36 (57993) hydrogen bonds : bond 0.05222 / 3.50 ( 2592) hydrogen bonds : angle 4.52093 / 3.24 ( 7244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9064 (mmp) cc_final: 0.8613 (mmm) REVERT: I 510 MET cc_start: 0.8737 (tpp) cc_final: 0.7941 (tpp) REVERT: I 514 MET cc_start: 0.7835 (ptt) cc_final: 0.6989 (ptt) REVERT: K 31 MET cc_start: 0.9250 (ptm) cc_final: 0.8989 (ptm) REVERT: K 35 MET cc_start: 0.9217 (mmt) cc_final: 0.8583 (mmm) REVERT: K 97 PHE cc_start: 0.9360 (m-10) cc_final: 0.9056 (m-10) REVERT: K 136 MET cc_start: 0.9379 (tpt) cc_final: 0.9008 (tpp) REVERT: K 166 MET cc_start: 0.9218 (mmt) cc_final: 0.8840 (mmt) REVERT: M 31 LEU cc_start: 0.9539 (tt) cc_final: 0.8944 (tt) REVERT: M 35 MET cc_start: 0.9206 (mmm) cc_final: 0.8745 (mmm) REVERT: M 107 GLU cc_start: 0.9405 (pm20) cc_final: 0.9184 (pm20) REVERT: N 331 MET cc_start: 0.8757 (tpp) cc_final: 0.8361 (tpp) REVERT: Q 88 MET cc_start: 0.9664 (ppp) cc_final: 0.9215 (ppp) REVERT: Q 165 MET cc_start: 0.9468 (mtm) cc_final: 0.8873 (ttm) REVERT: U 320 MET cc_start: 0.9519 (ttt) cc_final: 0.9034 (tpp) REVERT: T 470 TYR cc_start: 0.9415 (m-80) cc_final: 0.9054 (m-10) REVERT: T 475 MET cc_start: 0.7897 (pmm) cc_final: 0.7591 (pmm) REVERT: T 478 LYS cc_start: 0.9724 (mmtt) cc_final: 0.9335 (tptp) REVERT: S 40 MET cc_start: 0.8206 (tpt) cc_final: 0.7333 (tpp) REVERT: S 55 PHE cc_start: 0.9513 (m-80) cc_final: 0.9199 (m-80) REVERT: d 84 MET cc_start: 0.4680 (ptt) cc_final: 0.4360 (ppp) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2148 time to fit residues: 57.2908 Evaluate side-chains 123 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 344 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 360 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.078102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.050063 restraints weight = 457976.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.050167 restraints weight = 294122.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050646 restraints weight = 194561.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050178 restraints weight = 164719.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.050272 restraints weight = 156770.171| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 41743 Z= 0.188 Angle : 0.629 11.019 57993 Z= 0.348 Chirality : 0.041 0.255 6603 Planarity : 0.004 0.058 5925 Dihedral : 25.441 178.862 8661 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 0.03 % Allowed : 0.79 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: 1.25 (0.14), residues: 3874 helix: 1.58 (0.10), residues: 2486 sheet: -0.74 (0.29), residues: 275 loop : -0.37 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 250 TYR 0.017 0.002 TYR f 83 PHE 0.031 0.002 PHE O 284 TRP 0.042 0.002 TRP K 239 HIS 0.009 0.001 HIS N 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (41743) covalent geometry : angle 0.62934 / 0.35 (57993) hydrogen bonds : bond 0.04911 / 3.29 ( 2592) hydrogen bonds : angle 4.48427 / 3.21 ( 7244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9066 (mmp) cc_final: 0.8613 (mmm) REVERT: I 224 ASP cc_start: 0.9594 (m-30) cc_final: 0.9385 (m-30) REVERT: I 510 MET cc_start: 0.8730 (tpp) cc_final: 0.7928 (tpp) REVERT: I 514 MET cc_start: 0.7826 (ptt) cc_final: 0.7007 (ptt) REVERT: K 35 MET cc_start: 0.9216 (mmt) cc_final: 0.8561 (mmm) REVERT: K 62 MET cc_start: 0.9595 (mmp) cc_final: 0.9376 (mmm) REVERT: K 97 PHE cc_start: 0.9338 (m-10) cc_final: 0.9025 (m-10) REVERT: K 136 MET cc_start: 0.9493 (tpt) cc_final: 0.9092 (tpp) REVERT: K 166 MET cc_start: 0.9223 (mmt) cc_final: 0.8837 (mmt) REVERT: M 31 LEU cc_start: 0.9526 (tt) cc_final: 0.8999 (tt) REVERT: M 35 MET cc_start: 0.9139 (mmm) cc_final: 0.8680 (mmm) REVERT: M 107 GLU cc_start: 0.9383 (pm20) cc_final: 0.9069 (pm20) REVERT: N 331 MET cc_start: 0.8802 (tpp) cc_final: 0.8419 (tpp) REVERT: Q 88 MET cc_start: 0.9662 (ppp) cc_final: 0.9249 (ppp) REVERT: Q 93 MET cc_start: 0.8439 (tpt) cc_final: 0.8063 (tmm) REVERT: Q 165 MET cc_start: 0.9461 (mtm) cc_final: 0.8855 (ttm) REVERT: Q 200 MET cc_start: 0.9014 (ptt) cc_final: 0.8418 (ptt) REVERT: U 320 MET cc_start: 0.9508 (ttt) cc_final: 0.9025 (tpp) REVERT: T 470 TYR cc_start: 0.9397 (m-80) cc_final: 0.9033 (m-10) REVERT: T 475 MET cc_start: 0.7854 (pmm) cc_final: 0.7630 (pmm) REVERT: T 478 LYS cc_start: 0.9717 (mmtt) cc_final: 0.9322 (tptp) REVERT: S 40 MET cc_start: 0.8134 (tpt) cc_final: 0.7271 (tpp) REVERT: S 55 PHE cc_start: 0.9502 (m-80) cc_final: 0.9201 (m-80) REVERT: d 84 MET cc_start: 0.4617 (ptt) cc_final: 0.4143 (ppp) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.2230 time to fit residues: 58.2807 Evaluate side-chains 122 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 242 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 326 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 410 HIS ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 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 = 0.4003 r_free = 0.4003 target = 0.079167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051087 restraints weight = 454092.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.050572 restraints weight = 290538.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.051777 restraints weight = 215538.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.051180 restraints weight = 160807.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.051316 restraints weight = 137160.938| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41743 Z= 0.138 Angle : 0.604 10.543 57993 Z= 0.334 Chirality : 0.041 0.251 6603 Planarity : 0.004 0.055 5925 Dihedral : 25.375 176.687 8661 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.44 (0.14), residues: 3874 helix: 1.73 (0.10), residues: 2486 sheet: -0.61 (0.29), residues: 276 loop : -0.31 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 520 TYR 0.016 0.002 TYR i 50 PHE 0.026 0.002 PHE O 284 TRP 0.062 0.002 TRP N 132 HIS 0.011 0.001 HIS N 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (41743) covalent geometry : angle 0.60410 / 0.33 (57993) hydrogen bonds : bond 0.04465 / 2.99 ( 2592) hydrogen bonds : angle 4.32156 / 3.09 ( 7244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9029 (mmp) cc_final: 0.8537 (mmm) REVERT: H 189 MET cc_start: 0.9050 (mtp) cc_final: 0.8560 (ptp) REVERT: H 247 MET cc_start: 0.6011 (tmm) cc_final: 0.5750 (tmm) REVERT: I 499 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9312 (mm-30) REVERT: I 510 MET cc_start: 0.8701 (tpp) cc_final: 0.7795 (tpp) REVERT: I 514 MET cc_start: 0.7778 (ptt) cc_final: 0.6695 (ptt) REVERT: K 31 MET cc_start: 0.9245 (ptm) cc_final: 0.8602 (ppp) REVERT: K 35 MET cc_start: 0.9138 (mmt) cc_final: 0.8420 (mmm) REVERT: K 97 PHE cc_start: 0.9351 (m-10) cc_final: 0.9028 (m-10) REVERT: K 136 MET cc_start: 0.9517 (tpt) cc_final: 0.9247 (tpp) REVERT: K 166 MET cc_start: 0.9232 (mmt) cc_final: 0.8818 (mmt) REVERT: M 31 LEU cc_start: 0.9553 (tt) cc_final: 0.9028 (tt) REVERT: M 35 MET cc_start: 0.9066 (mmm) cc_final: 0.8581 (mmm) REVERT: M 107 GLU cc_start: 0.9335 (pm20) cc_final: 0.9000 (pm20) REVERT: L 230 MET cc_start: 0.7100 (tpt) cc_final: 0.5774 (tpp) REVERT: N 331 MET cc_start: 0.8825 (tpp) cc_final: 0.8375 (tpp) REVERT: Q 88 MET cc_start: 0.9663 (ppp) cc_final: 0.9197 (ppp) REVERT: Q 165 MET cc_start: 0.9476 (mtm) cc_final: 0.8973 (ttm) REVERT: Q 200 MET cc_start: 0.8937 (ptt) cc_final: 0.8167 (pmm) REVERT: U 320 MET cc_start: 0.9524 (ttt) cc_final: 0.9000 (tpp) REVERT: T 470 TYR cc_start: 0.9400 (m-80) cc_final: 0.9002 (m-10) REVERT: T 475 MET cc_start: 0.7794 (pmm) cc_final: 0.7536 (pmm) REVERT: T 478 LYS cc_start: 0.9743 (mmtt) cc_final: 0.9344 (tptp) REVERT: S 40 MET cc_start: 0.7970 (tpt) cc_final: 0.7155 (tpp) REVERT: S 55 PHE cc_start: 0.9438 (m-80) cc_final: 0.9143 (m-80) REVERT: d 84 MET cc_start: 0.4885 (ptt) cc_final: 0.4477 (ppp) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2300 time to fit residues: 61.7190 Evaluate side-chains 133 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 172 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 392 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 87 optimal weight: 0.0000 chunk 407 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 110 optimal weight: 0.0170 chunk 414 optimal weight: 30.0000 chunk 157 optimal weight: 4.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 HIS ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 284 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 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 = 0.4000 r_free = 0.4000 target = 0.079047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.052340 restraints weight = 454710.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051076 restraints weight = 307627.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051663 restraints weight = 216615.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051581 restraints weight = 159810.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051548 restraints weight = 161018.830| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41743 Z= 0.141 Angle : 0.598 12.166 57993 Z= 0.330 Chirality : 0.040 0.249 6603 Planarity : 0.003 0.054 5925 Dihedral : 25.330 176.309 8661 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.56 (0.14), residues: 3874 helix: 1.82 (0.10), residues: 2484 sheet: -0.56 (0.29), residues: 276 loop : -0.23 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 68 TYR 0.015 0.002 TYR i 50 PHE 0.023 0.002 PHE b 262 TRP 0.043 0.002 TRP K 239 HIS 0.007 0.001 HIS I 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (41743) covalent geometry : angle 0.59799 / 0.33 (57993) hydrogen bonds : bond 0.04458 / 2.98 ( 2592) hydrogen bonds : angle 4.27608 / 3.06 ( 7244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 MET cc_start: 0.9063 (mmp) cc_final: 0.8560 (mmm) REVERT: H 189 MET cc_start: 0.9049 (mtp) cc_final: 0.8547 (ptp) REVERT: H 247 MET cc_start: 0.5797 (tmm) cc_final: 0.4773 (ppp) REVERT: I 499 GLU cc_start: 0.9522 (mt-10) cc_final: 0.9299 (mm-30) REVERT: I 510 MET cc_start: 0.8688 (tpp) cc_final: 0.8110 (tpp) REVERT: I 514 MET cc_start: 0.7785 (ptt) cc_final: 0.6682 (ptt) REVERT: K 35 MET cc_start: 0.9238 (mmt) cc_final: 0.8582 (mmm) REVERT: K 97 PHE cc_start: 0.9339 (m-10) cc_final: 0.9021 (m-10) REVERT: K 136 MET cc_start: 0.9506 (tpt) cc_final: 0.9228 (tpp) REVERT: K 166 MET cc_start: 0.9216 (mmt) cc_final: 0.8857 (mmt) REVERT: M 31 LEU cc_start: 0.9545 (tt) cc_final: 0.9029 (tt) REVERT: M 35 MET cc_start: 0.9050 (mmm) cc_final: 0.8595 (mmm) REVERT: M 107 GLU cc_start: 0.9373 (pm20) cc_final: 0.9020 (pm20) REVERT: L 230 MET cc_start: 0.6969 (tpt) cc_final: 0.5626 (tpp) REVERT: N 88 MET cc_start: 0.9051 (mmm) cc_final: 0.8837 (mmm) REVERT: N 331 MET cc_start: 0.8785 (tpp) cc_final: 0.8277 (tpp) REVERT: Q 88 MET cc_start: 0.9655 (ppp) cc_final: 0.9209 (ppp) REVERT: Q 165 MET cc_start: 0.9471 (mtm) cc_final: 0.8872 (ttm) REVERT: Q 200 MET cc_start: 0.8979 (ptt) cc_final: 0.8211 (pmm) REVERT: U 320 MET cc_start: 0.9535 (ttt) cc_final: 0.9018 (tpp) REVERT: T 470 TYR cc_start: 0.9395 (m-80) cc_final: 0.9042 (m-10) REVERT: T 473 MET cc_start: 0.9313 (tpp) cc_final: 0.9053 (tpp) REVERT: T 475 MET cc_start: 0.7885 (pmm) cc_final: 0.7611 (pmm) REVERT: S 40 MET cc_start: 0.8116 (tpt) cc_final: 0.7322 (tpp) REVERT: S 55 PHE cc_start: 0.9427 (m-80) cc_final: 0.9135 (m-80) REVERT: S 67 MET cc_start: 0.9059 (ptp) cc_final: 0.8764 (ptp) REVERT: d 84 MET cc_start: 0.4377 (ptt) cc_final: 0.3983 (ppp) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2249 time to fit residues: 60.1310 Evaluate side-chains 126 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 108 optimal weight: 5.9990 chunk 327 optimal weight: 70.0000 chunk 152 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 284 optimal weight: 4.9990 chunk 339 optimal weight: 50.0000 chunk 72 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 ASN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 GLN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN ** N 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.077424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.049594 restraints weight = 462533.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.048981 restraints weight = 295633.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.049571 restraints weight = 207645.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.049320 restraints weight = 178084.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049629 restraints weight = 165006.518| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 41743 Z= 0.243 Angle : 0.678 10.950 57993 Z= 0.371 Chirality : 0.041 0.263 6603 Planarity : 0.004 0.057 5925 Dihedral : 25.426 179.844 8661 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.24 (0.14), residues: 3874 helix: 1.57 (0.10), residues: 2489 sheet: -0.79 (0.29), residues: 279 loop : -0.36 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 68 TYR 0.022 0.002 TYR d 88 PHE 0.029 0.003 PHE b 262 TRP 0.046 0.002 TRP N 132 HIS 0.024 0.002 HIS M 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.24 (41743) covalent geometry : angle 0.67769 / 0.37 (57993) hydrogen bonds : bond 0.05398 / 3.62 ( 2592) hydrogen bonds : angle 4.48369 / 3.21 ( 7244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7865.03 seconds wall clock time: 136 minutes 41.20 seconds (8201.20 seconds total)