Starting phenix.real_space_refine on Sat Jul 4 04:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vlq_65163/07_2026/9vlq_65163_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vlq_65163/07_2026/9vlq_65163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vlq_65163/07_2026/9vlq_65163_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vlq_65163/07_2026/9vlq_65163_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vlq_65163/07_2026/9vlq_65163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vlq_65163/07_2026/9vlq_65163.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 11237 2.51 5 N 3124 2.21 5 O 3198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17638 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 6028 Classifications: {'peptide': 759} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 731} Chain breaks: 3 Chain: "B" Number of atoms: 5633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5633 Classifications: {'peptide': 748} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 687} Chain: "C" Number of atoms: 5849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5849 Classifications: {'peptide': 762} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 708} Chain breaks: 4 Chain: "X" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.01, per 1000 atoms: 0.23 Number of scatterers: 17638 At special positions: 0 Unit cell: (110.04, 115.92, 203.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 7 15.00 Mg 1 11.99 O 3198 8.00 N 3124 7.00 C 11237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 469 " distance=2.04 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: 1.43 Conformation dependent library (CDL) restraints added in 767.2 milliseconds 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 19 sheets defined 49.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.841A pdb=" N PHE A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N HIS A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 67 through 77 removed outlier: 4.141A pdb=" N PHE A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.624A pdb=" N GLY A 82 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 83' Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.625A pdb=" N VAL A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 removed outlier: 3.656A pdb=" N ALA A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.949A pdb=" N PHE A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.597A pdb=" N VAL A 156 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.569A pdb=" N LEU A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.304A pdb=" N ASP A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.505A pdb=" N LEU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 4.396A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.525A pdb=" N HIS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.523A pdb=" N ARG A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 256 No H-bonds generated for 'chain 'A' and resid 255 through 256' Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.632A pdb=" N VAL A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.629A pdb=" N ARG A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.726A pdb=" N MET A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 397 through 415 removed outlier: 3.519A pdb=" N ALA A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 443 removed outlier: 5.020A pdb=" N GLU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.619A pdb=" N TRP A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.372A pdb=" N THR A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.834A pdb=" N PHE A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 533 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.727A pdb=" N GLY A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 566 through 585 removed outlier: 3.666A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 685 removed outlier: 4.508A pdb=" N GLN A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 680 " --> pdb=" O ARG A 676 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 682 " --> pdb=" O ARG A 678 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 745 removed outlier: 3.684A pdb=" N GLU A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 759 removed outlier: 3.501A pdb=" N LEU A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 839 Processing helix chain 'A' and resid 853 through 857 removed outlier: 3.823A pdb=" N GLU A 857 " --> pdb=" O PRO A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.937A pdb=" N ASP A 875 " --> pdb=" O ALA A 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 70 through 81 Processing helix chain 'B' and resid 94 through 113 removed outlier: 3.692A pdb=" N GLU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.642A pdb=" N GLU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.830A pdb=" N ILE B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 192 removed outlier: 3.769A pdb=" N ALA B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 192' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.792A pdb=" N ASP B 228 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 removed outlier: 3.566A pdb=" N LEU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.874A pdb=" N GLU B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 343 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 353 through 356 removed outlier: 3.959A pdb=" N VAL B 356 " --> pdb=" O ALA B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 356' Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 361 through 371 removed outlier: 3.793A pdb=" N GLY B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 removed outlier: 3.567A pdb=" N GLU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 removed outlier: 3.633A pdb=" N ALA B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 431 removed outlier: 4.280A pdb=" N ASP B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 removed outlier: 3.845A pdb=" N ARG B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU B 441 " --> pdb=" O GLY B 437 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 460 removed outlier: 4.080A pdb=" N GLY B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.877A pdb=" N CYS B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 494 removed outlier: 3.614A pdb=" N SER B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 542 removed outlier: 3.880A pdb=" N ALA B 520 " --> pdb=" O ASP B 516 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.559A pdb=" N THR B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 596 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 604 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 637 removed outlier: 3.531A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 660 through 666 Processing helix chain 'B' and resid 667 through 673 removed outlier: 3.939A pdb=" N ALA B 672 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 673 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 697 No H-bonds generated for 'chain 'B' and resid 695 through 697' Processing helix chain 'B' and resid 707 through 731 Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.785A pdb=" N LEU C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.503A pdb=" N LEU C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 134 removed outlier: 3.801A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.663A pdb=" N ILE C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.923A pdb=" N LEU C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HIS C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 168 removed outlier: 3.967A pdb=" N ASN C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 209 removed outlier: 3.533A pdb=" N HIS C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.525A pdb=" N VAL C 213 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 238 through 250 removed outlier: 4.648A pdb=" N THR C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 removed outlier: 4.235A pdb=" N ARG C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.702A pdb=" N ALA C 261 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 262 " --> pdb=" O ALA C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 262' Processing helix chain 'C' and resid 264 through 274 removed outlier: 3.507A pdb=" N ILE C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.571A pdb=" N SER C 290 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 287 through 291' Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.629A pdb=" N ARG C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY C 309 " --> pdb=" O TYR C 306 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ALA C 310 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 311 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 331 removed outlier: 4.124A pdb=" N GLU C 320 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 347 through 361 removed outlier: 4.363A pdb=" N THR C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 376 Processing helix chain 'C' and resid 391 through 403 Processing helix chain 'C' and resid 409 through 418 removed outlier: 3.593A pdb=" N TYR C 413 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.530A pdb=" N THR C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 499 through 510 Processing helix chain 'C' and resid 519 through 525 removed outlier: 4.169A pdb=" N LEU C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.519A pdb=" N ILE C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 Processing helix chain 'C' and resid 578 through 593 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 638 through 661 Processing helix chain 'C' and resid 776 through 793 Processing helix chain 'C' and resid 795 through 802 Processing helix chain 'C' and resid 852 through 860 removed outlier: 3.668A pdb=" N HIS C 860 " --> pdb=" O PHE C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 866 removed outlier: 6.003A pdb=" N ARG C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 866 " --> pdb=" O PRO C 863 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.864A pdb=" N ALA A 91 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N CYS A 288 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 249 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN A 143 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.678A pdb=" N PHE A 340 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 394 removed outlier: 5.848A pdb=" N THR A 392 " --> pdb=" O ALA A 822 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 422 through 424 removed outlier: 3.656A pdb=" N PHE A 423 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 494 " --> pdb=" O PHE A 423 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 489 removed outlier: 4.616A pdb=" N LEU A 428 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 798 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 430 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 796 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 707 removed outlier: 5.613A pdb=" N VAL A 765 " --> pdb=" O MET A 729 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR A 731 " --> pdb=" O TYR A 763 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR A 763 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 764 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 775 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A 510 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 716 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 706 through 707 removed outlier: 6.198A pdb=" N ASP A 724 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL A 502 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.517A pdb=" N ALA B 51 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 55 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 31 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR B 30 " --> pdb=" O TRP B 22 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N TRP B 22 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N HIS B 32 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA B 20 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU B 34 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU B 18 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR B 36 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE B 16 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL B 38 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AB1, first strand: chain 'B' and resid 154 through 157 removed outlier: 3.811A pdb=" N SER B 196 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 231 through 237 removed outlier: 3.678A pdb=" N VAL B 235 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 246 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB4, first strand: chain 'B' and resid 398 through 400 removed outlier: 3.834A pdb=" N ALA B 561 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 497 through 501 removed outlier: 6.609A pdb=" N TRP B 507 " --> pdb=" O CYS B 499 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 501 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 508 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 406 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 556 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 409 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU B 554 " --> pdb=" O CYS B 409 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 648 through 650 removed outlier: 3.649A pdb=" N VAL B 648 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 677 " --> pdb=" O VAL B 650 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.851A pdb=" N ILE C 50 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 25 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 20 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N CYS C 94 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 22 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU C 96 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N TYR C 24 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 95 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 421 through 425 removed outlier: 3.572A pdb=" N SER C 886 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 423 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU C 884 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU C 425 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARG C 882 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL C 773 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER C 886 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 455 removed outlier: 6.885A pdb=" N CYS C 451 " --> pdb=" O ALA C 551 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL C 535 " --> pdb=" O ILE C 615 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 626 through 629 removed outlier: 4.098A pdb=" N PHE C 675 " --> pdb=" O VAL C 843 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5868 1.34 - 1.47: 4550 1.47 - 1.61: 7555 1.61 - 1.74: 7 1.74 - 1.87: 100 Bond restraints: 18080 Sorted by residual: bond pdb=" CA CYS A 106 " pdb=" C CYS A 106 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.44e-02 4.82e+03 9.16e+00 bond pdb=" CA LYS A 103 " pdb=" C LYS A 103 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.24e-02 6.50e+03 7.57e+00 bond pdb=" C1' DT X 1 " pdb=" N1 DT X 1 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.97e+00 bond pdb=" C CYS A 106 " pdb=" N VAL A 107 " ideal model delta sigma weight residual 1.335 1.308 0.028 1.23e-02 6.61e+03 5.07e+00 bond pdb=" CA GLU A 315 " pdb=" C GLU A 315 " ideal model delta sigma weight residual 1.528 1.504 0.024 1.07e-02 8.73e+03 4.95e+00 ... (remaining 18075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 24345 1.87 - 3.74: 278 3.74 - 5.61: 46 5.61 - 7.48: 8 7.48 - 9.35: 1 Bond angle restraints: 24678 Sorted by residual: angle pdb=" N LYS A 103 " pdb=" CA LYS A 103 " pdb=" C LYS A 103 " ideal model delta sigma weight residual 110.97 106.44 4.53 1.09e+00 8.42e-01 1.73e+01 angle pdb=" N3 DT X 3 " pdb=" C4 DT X 3 " pdb=" O4 DT X 3 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT X 1 " pdb=" C4 DT X 1 " pdb=" O4 DT X 1 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" CA CYS B 469 " pdb=" CB CYS B 469 " pdb=" SG CYS B 469 " ideal model delta sigma weight residual 114.40 123.75 -9.35 2.30e+00 1.89e-01 1.65e+01 angle pdb=" N3 DT X 5 " pdb=" C4 DT X 5 " pdb=" O4 DT X 5 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 24673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9622 17.75 - 35.49: 854 35.49 - 53.24: 183 53.24 - 70.99: 45 70.99 - 88.73: 14 Dihedral angle restraints: 10718 sinusoidal: 4152 harmonic: 6566 Sorted by residual: dihedral pdb=" CA PRO A 692 " pdb=" C PRO A 692 " pdb=" N PHE A 693 " pdb=" CA PHE A 693 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA CYS B 466 " pdb=" C CYS B 466 " pdb=" N ASN B 467 " pdb=" CA ASN B 467 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA THR A 462 " pdb=" C THR A 462 " pdb=" N ASN A 463 " pdb=" CA ASN A 463 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 10715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1927 0.034 - 0.068: 610 0.068 - 0.102: 182 0.102 - 0.136: 68 0.136 - 0.169: 4 Chirality restraints: 2791 Sorted by residual: chirality pdb=" CB THR A 659 " pdb=" CA THR A 659 " pdb=" OG1 THR A 659 " pdb=" CG2 THR A 659 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB THR A 295 " pdb=" CA THR A 295 " pdb=" OG1 THR A 295 " pdb=" CG2 THR A 295 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CB ILE A 549 " pdb=" CA ILE A 549 " pdb=" CG1 ILE A 549 " pdb=" CG2 ILE A 549 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 2788 not shown) Planarity restraints: 3195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 770 " 0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO C 771 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 771 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 771 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 691 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 692 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 692 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 692 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 875 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 876 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 876 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 876 " 0.026 5.00e-02 4.00e+02 ... (remaining 3192 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 186 2.63 - 3.20: 15452 3.20 - 3.76: 27551 3.76 - 4.33: 36276 4.33 - 4.90: 59871 Nonbonded interactions: 139336 Sorted by model distance: nonbonded pdb=" O3B ADP A 901 " pdb="MG MG A 902 " model vdw 2.061 2.170 nonbonded pdb=" OG1 THR C 21 " pdb=" NH2 ARG C 255 " model vdw 2.248 3.120 nonbonded pdb=" OG1 THR A 532 " pdb=" OE1 GLN A 533 " model vdw 2.250 3.040 nonbonded pdb=" O1B ADP A 901 " pdb="MG MG A 902 " model vdw 2.255 2.170 nonbonded pdb=" NH2 ARG A 123 " pdb=" OP2 DT X 3 " model vdw 2.265 3.120 ... (remaining 139331 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.850 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.002 0.057 18081 Z= 0.120 Angle : 0.494 9.352 24680 Z= 0.265 Chirality : 0.039 0.169 2791 Planarity : 0.004 0.064 3195 Dihedral : 14.597 88.734 6485 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.50 % Allowed : 0.28 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2249 helix: 0.62 (0.19), residues: 846 sheet: -0.64 (0.33), residues: 286 loop : -1.02 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.020 0.001 TYR A 439 PHE 0.023 0.001 PHE A 673 TRP 0.007 0.001 TRP B 348 HIS 0.002 0.000 HIS C 885 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (18080) covalent geometry : angle 0.48995 / 0.26 (24678) SS BOND : bond 0.00493 / 0.31 ( 1) SS BOND : angle 6.61060 / 3.11 ( 2) hydrogen bonds : bond 0.26626 / 18.14 ( 706) hydrogen bonds : angle 7.57268 / 5.33 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7586 (mtt) cc_final: 0.7361 (mtt) REVERT: A 559 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.6188 (t80) REVERT: A 580 LEU cc_start: 0.8618 (mt) cc_final: 0.8345 (mt) REVERT: A 713 ARG cc_start: 0.6893 (mmm-85) cc_final: 0.6605 (tmm160) REVERT: A 794 MET cc_start: 0.4287 (mmt) cc_final: 0.3997 (mmm) REVERT: A 848 LEU cc_start: 0.8777 (tp) cc_final: 0.8551 (pt) REVERT: B 19 TYR cc_start: 0.5708 (t80) cc_final: 0.5417 (t80) REVERT: B 135 LYS cc_start: 0.6616 (tppt) cc_final: 0.6259 (mmmm) REVERT: B 188 THR cc_start: 0.8397 (m) cc_final: 0.7989 (t) REVERT: B 210 ARG cc_start: 0.6414 (mmt-90) cc_final: 0.6085 (mpt180) REVERT: C 93 PHE cc_start: 0.7463 (m-10) cc_final: 0.7218 (m-10) REVERT: C 158 MET cc_start: 0.7796 (tpt) cc_final: 0.7368 (tpt) REVERT: C 460 MET cc_start: 0.8138 (tpp) cc_final: 0.7622 (tpp) REVERT: C 561 ASP cc_start: 0.6194 (t0) cc_final: 0.5710 (t0) REVERT: C 597 MET cc_start: 0.3562 (tpt) cc_final: 0.2936 (tpt) outliers start: 9 outliers final: 1 residues processed: 275 average time/residue: 0.1860 time to fit residues: 70.9813 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 559 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS A 663 HIS A 751 ASN ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 157 ASN C 417 ASN C 775 HIS C 885 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.118861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.093309 restraints weight = 51906.500| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.06 r_work: 0.3536 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 18081 Z= 0.340 Angle : 0.813 15.920 24680 Z= 0.422 Chirality : 0.051 0.182 2791 Planarity : 0.007 0.081 3195 Dihedral : 7.219 86.714 2576 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.36 % Favored : 91.55 % Rotamer: Outliers : 1.50 % Allowed : 12.44 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.43 (0.18), residues: 2249 helix: -0.09 (0.17), residues: 930 sheet: -1.44 (0.28), residues: 351 loop : -1.53 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 503 TYR 0.042 0.003 TYR C 772 PHE 0.050 0.004 PHE C 479 TRP 0.036 0.003 TRP A 337 HIS 0.012 0.002 HIS B 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.34 (18080) covalent geometry : angle 0.81238 / 0.42 (24678) SS BOND : bond 0.03592 / 2.24 ( 1) SS BOND : angle 1.94682 / 0.89 ( 2) hydrogen bonds : bond 0.06608 / 4.62 ( 706) hydrogen bonds : angle 5.74623 / 4.06 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 PHE cc_start: 0.7761 (t80) cc_final: 0.7191 (m-80) REVERT: A 717 MET cc_start: 0.5097 (ptp) cc_final: 0.3546 (ppp) REVERT: A 773 MET cc_start: 0.6025 (mtm) cc_final: 0.5148 (mpp) REVERT: A 794 MET cc_start: 0.4036 (mmt) cc_final: 0.3824 (mmm) REVERT: B 19 TYR cc_start: 0.6331 (t80) cc_final: 0.5875 (t80) REVERT: B 47 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6912 (mtp85) REVERT: B 55 VAL cc_start: 0.8419 (m) cc_final: 0.8176 (t) REVERT: B 135 LYS cc_start: 0.6913 (tppt) cc_final: 0.6604 (mmmm) REVERT: B 163 MET cc_start: 0.8020 (tmm) cc_final: 0.7663 (tmm) REVERT: B 188 THR cc_start: 0.8500 (m) cc_final: 0.8276 (t) REVERT: B 217 PHE cc_start: 0.7253 (m-10) cc_final: 0.7046 (m-10) REVERT: C 113 MET cc_start: 0.8073 (tpt) cc_final: 0.7597 (tpt) REVERT: C 131 LEU cc_start: 0.7593 (mt) cc_final: 0.7392 (mp) REVERT: C 158 MET cc_start: 0.7957 (tpt) cc_final: 0.7524 (tpt) REVERT: C 300 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8077 (t80) REVERT: C 560 ARG cc_start: 0.8068 (ptp90) cc_final: 0.7767 (ptp90) REVERT: C 597 MET cc_start: 0.4372 (tpt) cc_final: 0.3156 (tpt) outliers start: 27 outliers final: 16 residues processed: 185 average time/residue: 0.1613 time to fit residues: 42.9428 Evaluate side-chains 146 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 874 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 0.0050 chunk 93 optimal weight: 3.9990 chunk 192 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 HIS A 725 ASN ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.095992 restraints weight = 51577.119| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.69 r_work: 0.3552 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18081 Z= 0.172 Angle : 0.608 11.783 24680 Z= 0.312 Chirality : 0.043 0.175 2791 Planarity : 0.005 0.059 3195 Dihedral : 6.902 84.970 2576 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.20 % Favored : 92.75 % Rotamer: Outliers : 2.44 % Allowed : 15.11 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 2249 helix: 0.50 (0.17), residues: 918 sheet: -1.45 (0.28), residues: 329 loop : -1.37 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 665 TYR 0.018 0.001 TYR C 221 PHE 0.027 0.002 PHE C 300 TRP 0.015 0.001 TRP B 507 HIS 0.008 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (18080) covalent geometry : angle 0.60615 / 0.31 (24678) SS BOND : bond 0.00512 / 0.32 ( 1) SS BOND : angle 4.54411 / 1.69 ( 2) hydrogen bonds : bond 0.05221 / 3.67 ( 706) hydrogen bonds : angle 5.21335 / 3.70 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 355 MET cc_start: 0.7051 (ptt) cc_final: 0.6748 (ptt) REVERT: A 489 ARG cc_start: 0.7882 (ptt-90) cc_final: 0.7012 (ptt-90) REVERT: A 520 PHE cc_start: 0.7781 (t80) cc_final: 0.7120 (m-80) REVERT: A 549 ILE cc_start: 0.7111 (mt) cc_final: 0.6803 (mt) REVERT: A 717 MET cc_start: 0.5231 (ptp) cc_final: 0.3759 (ppp) REVERT: A 773 MET cc_start: 0.6336 (mtm) cc_final: 0.5536 (mpp) REVERT: A 794 MET cc_start: 0.4074 (mmp) cc_final: 0.3826 (mmm) REVERT: A 869 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 19 TYR cc_start: 0.6379 (t80) cc_final: 0.5926 (t80) REVERT: B 47 ARG cc_start: 0.7515 (mtp85) cc_final: 0.7047 (mtp85) REVERT: B 135 LYS cc_start: 0.6868 (tppt) cc_final: 0.6568 (mmmm) REVERT: B 163 MET cc_start: 0.8152 (tmm) cc_final: 0.7845 (tmm) REVERT: B 188 THR cc_start: 0.8477 (m) cc_final: 0.8246 (t) REVERT: B 217 PHE cc_start: 0.7226 (m-10) cc_final: 0.6940 (m-10) REVERT: B 610 THR cc_start: 0.5746 (OUTLIER) cc_final: 0.5533 (p) REVERT: B 630 ASP cc_start: 0.8364 (t0) cc_final: 0.8158 (m-30) REVERT: C 93 PHE cc_start: 0.7999 (m-10) cc_final: 0.7468 (m-10) REVERT: C 113 MET cc_start: 0.7928 (tpt) cc_final: 0.7103 (tpt) REVERT: C 131 LEU cc_start: 0.7552 (mt) cc_final: 0.7342 (mp) REVERT: C 158 MET cc_start: 0.7757 (tpt) cc_final: 0.7381 (tpt) REVERT: C 460 MET cc_start: 0.8427 (tpp) cc_final: 0.8138 (tpp) REVERT: C 560 ARG cc_start: 0.7964 (ptp90) cc_final: 0.7686 (ptp90) REVERT: C 597 MET cc_start: 0.4286 (tpt) cc_final: 0.3193 (tpt) REVERT: C 780 MET cc_start: 0.8509 (tpp) cc_final: 0.8065 (tpp) outliers start: 44 outliers final: 22 residues processed: 178 average time/residue: 0.1559 time to fit residues: 40.5386 Evaluate side-chains 153 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 874 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 156 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN A 294 GLN A 497 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 ASN ** 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 = 0.4207 r_free = 0.4207 target = 0.120927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.096544 restraints weight = 51661.563| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.42 r_work: 0.3584 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18081 Z= 0.136 Angle : 0.572 9.496 24680 Z= 0.292 Chirality : 0.042 0.190 2791 Planarity : 0.005 0.046 3195 Dihedral : 6.771 83.441 2576 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer: Outliers : 2.67 % Allowed : 16.61 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2249 helix: 0.62 (0.17), residues: 931 sheet: -1.49 (0.28), residues: 338 loop : -1.29 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 308 TYR 0.017 0.001 TYR B 30 PHE 0.031 0.002 PHE C 300 TRP 0.014 0.001 TRP B 507 HIS 0.009 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (18080) covalent geometry : angle 0.56940 / 0.29 (24678) SS BOND : bond 0.01136 / 0.71 ( 1) SS BOND : angle 6.41705 / 2.95 ( 2) hydrogen bonds : bond 0.04315 / 3.03 ( 706) hydrogen bonds : angle 4.95908 / 3.52 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: A 489 ARG cc_start: 0.7865 (ptt-90) cc_final: 0.7505 (ptt-90) REVERT: A 520 PHE cc_start: 0.7495 (t80) cc_final: 0.7012 (m-80) REVERT: A 562 ARG cc_start: 0.5965 (tmt170) cc_final: 0.5683 (tmt170) REVERT: A 693 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.6009 (t80) REVERT: A 717 MET cc_start: 0.5342 (ptp) cc_final: 0.3843 (ppp) REVERT: A 773 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.5676 (mpp) REVERT: A 794 MET cc_start: 0.4296 (mmp) cc_final: 0.4021 (mmm) REVERT: A 802 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.6941 (mt) REVERT: A 848 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8622 (pp) REVERT: A 850 MET cc_start: 0.7993 (pmm) cc_final: 0.7585 (pmm) REVERT: A 869 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 19 TYR cc_start: 0.6350 (t80) cc_final: 0.5852 (t80) REVERT: B 47 ARG cc_start: 0.7431 (mtp85) cc_final: 0.6960 (mtp85) REVERT: B 135 LYS cc_start: 0.6897 (tppt) cc_final: 0.6578 (mmmm) REVERT: B 163 MET cc_start: 0.8170 (tmm) cc_final: 0.7824 (tmm) REVERT: B 188 THR cc_start: 0.8437 (m) cc_final: 0.8210 (t) REVERT: B 214 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6463 (m) REVERT: B 217 PHE cc_start: 0.7105 (m-10) cc_final: 0.6836 (m-10) REVERT: B 467 ASN cc_start: 0.8176 (t0) cc_final: 0.7891 (t0) REVERT: B 476 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7906 (mt) REVERT: B 610 THR cc_start: 0.5744 (OUTLIER) cc_final: 0.5539 (p) REVERT: B 630 ASP cc_start: 0.8299 (t0) cc_final: 0.8097 (m-30) REVERT: C 113 MET cc_start: 0.7905 (tpt) cc_final: 0.7654 (tpt) REVERT: C 117 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7220 (tpp80) REVERT: C 131 LEU cc_start: 0.7486 (mt) cc_final: 0.7273 (mp) REVERT: C 158 MET cc_start: 0.7851 (tpt) cc_final: 0.7491 (tpt) REVERT: C 460 MET cc_start: 0.8406 (tpp) cc_final: 0.8176 (tpp) REVERT: C 560 ARG cc_start: 0.7911 (ptp90) cc_final: 0.7627 (ptp90) REVERT: C 597 MET cc_start: 0.4357 (tpt) cc_final: 0.3236 (tpt) REVERT: C 780 MET cc_start: 0.8521 (tpp) cc_final: 0.8198 (tpp) outliers start: 48 outliers final: 23 residues processed: 173 average time/residue: 0.1560 time to fit residues: 39.7440 Evaluate side-chains 152 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 824 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 143 optimal weight: 0.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 ASN A 497 ASN A 725 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.121637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.097423 restraints weight = 51408.564| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.76 r_work: 0.3553 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18081 Z= 0.121 Angle : 0.549 13.766 24680 Z= 0.279 Chirality : 0.041 0.257 2791 Planarity : 0.005 0.054 3195 Dihedral : 6.695 82.968 2576 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 2.39 % Allowed : 18.06 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2249 helix: 0.73 (0.18), residues: 934 sheet: -1.46 (0.28), residues: 332 loop : -1.28 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 441 TYR 0.018 0.001 TYR B 30 PHE 0.026 0.001 PHE C 300 TRP 0.013 0.001 TRP B 507 HIS 0.007 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (18080) covalent geometry : angle 0.54712 / 0.28 (24678) SS BOND : bond 0.01653 / 1.03 ( 1) SS BOND : angle 5.40336 / 2.53 ( 2) hydrogen bonds : bond 0.03839 / 2.71 ( 706) hydrogen bonds : angle 4.85429 / 3.40 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: A 520 PHE cc_start: 0.7478 (t80) cc_final: 0.7161 (t80) REVERT: A 562 ARG cc_start: 0.6001 (tmt170) cc_final: 0.5717 (tmt170) REVERT: A 717 MET cc_start: 0.5372 (ptp) cc_final: 0.3850 (ppp) REVERT: A 773 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5597 (mpp) REVERT: A 794 MET cc_start: 0.3971 (mmp) cc_final: 0.3723 (mmm) REVERT: A 848 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 850 MET cc_start: 0.7989 (pmm) cc_final: 0.7576 (pmm) REVERT: A 869 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 19 TYR cc_start: 0.6413 (t80) cc_final: 0.5862 (t80) REVERT: B 32 HIS cc_start: 0.7228 (m170) cc_final: 0.6809 (m90) REVERT: B 47 ARG cc_start: 0.7456 (mtp85) cc_final: 0.6959 (mtp85) REVERT: B 112 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6336 (mp-120) REVERT: B 135 LYS cc_start: 0.6889 (tppt) cc_final: 0.6537 (mmmm) REVERT: B 137 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6732 (mm-30) REVERT: B 163 MET cc_start: 0.8256 (tmm) cc_final: 0.7924 (tmm) REVERT: B 188 THR cc_start: 0.8463 (m) cc_final: 0.8216 (t) REVERT: B 217 PHE cc_start: 0.7199 (m-10) cc_final: 0.6860 (m-10) REVERT: B 467 ASN cc_start: 0.8054 (t0) cc_final: 0.7769 (t0) REVERT: B 610 THR cc_start: 0.5713 (OUTLIER) cc_final: 0.5497 (p) REVERT: C 113 MET cc_start: 0.7827 (tpt) cc_final: 0.7165 (tpt) REVERT: C 117 ARG cc_start: 0.7805 (tpp80) cc_final: 0.7444 (mmt90) REVERT: C 131 LEU cc_start: 0.7476 (mt) cc_final: 0.7169 (mp) REVERT: C 158 MET cc_start: 0.7923 (tpt) cc_final: 0.7534 (tpt) REVERT: C 460 MET cc_start: 0.8447 (tpp) cc_final: 0.8153 (tpp) REVERT: C 560 ARG cc_start: 0.7931 (ptp90) cc_final: 0.7550 (ptp90) REVERT: C 597 MET cc_start: 0.4239 (tpt) cc_final: 0.3551 (tpt) REVERT: C 665 ARG cc_start: 0.7919 (tpp-160) cc_final: 0.7655 (mmm160) outliers start: 43 outliers final: 23 residues processed: 159 average time/residue: 0.1679 time to fit residues: 38.7561 Evaluate side-chains 142 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 86 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 725 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 HIS ** 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 = 0.4203 r_free = 0.4203 target = 0.120490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.096979 restraints weight = 50881.289| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.76 r_work: 0.3556 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18081 Z= 0.147 Angle : 0.565 12.000 24680 Z= 0.286 Chirality : 0.042 0.191 2791 Planarity : 0.004 0.047 3195 Dihedral : 6.729 83.809 2576 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.47 % Favored : 92.49 % Rotamer: Outliers : 3.06 % Allowed : 18.17 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2249 helix: 0.74 (0.18), residues: 933 sheet: -1.53 (0.28), residues: 332 loop : -1.30 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 489 TYR 0.022 0.001 TYR C 53 PHE 0.029 0.002 PHE C 363 TRP 0.011 0.001 TRP B 507 HIS 0.006 0.001 HIS B 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (18080) covalent geometry : angle 0.56299 / 0.29 (24678) SS BOND : bond 0.01664 / 1.04 ( 1) SS BOND : angle 5.02870 / 2.02 ( 2) hydrogen bonds : bond 0.03941 / 2.78 ( 706) hydrogen bonds : angle 4.80737 / 3.38 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 354 LEU cc_start: 0.7113 (pp) cc_final: 0.6457 (mp) REVERT: A 478 GLU cc_start: 0.4000 (OUTLIER) cc_final: 0.3161 (tp30) REVERT: A 520 PHE cc_start: 0.7240 (t80) cc_final: 0.6990 (t80) REVERT: A 562 ARG cc_start: 0.6044 (tmt170) cc_final: 0.5774 (tmt170) REVERT: A 717 MET cc_start: 0.5407 (ptp) cc_final: 0.3768 (ppp) REVERT: A 773 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.5598 (mpp) REVERT: A 794 MET cc_start: 0.4354 (mmp) cc_final: 0.4073 (mmm) REVERT: A 848 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 850 MET cc_start: 0.7979 (pmm) cc_final: 0.7556 (pmm) REVERT: A 869 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 32 HIS cc_start: 0.7272 (m170) cc_final: 0.6592 (m170) REVERT: B 47 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6930 (mtp85) REVERT: B 112 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6293 (mp-120) REVERT: B 135 LYS cc_start: 0.6883 (tppt) cc_final: 0.6510 (mmmm) REVERT: B 137 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6747 (mm-30) REVERT: B 163 MET cc_start: 0.8220 (tmm) cc_final: 0.7897 (tmm) REVERT: B 188 THR cc_start: 0.8470 (m) cc_final: 0.8243 (t) REVERT: B 217 PHE cc_start: 0.7206 (m-10) cc_final: 0.6891 (m-10) REVERT: B 467 ASN cc_start: 0.8057 (t0) cc_final: 0.7743 (t0) REVERT: B 610 THR cc_start: 0.5733 (OUTLIER) cc_final: 0.5519 (p) REVERT: C 113 MET cc_start: 0.7793 (tpt) cc_final: 0.7091 (tpt) REVERT: C 117 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7476 (mmt90) REVERT: C 131 LEU cc_start: 0.7387 (mt) cc_final: 0.7104 (mp) REVERT: C 158 MET cc_start: 0.7891 (tpt) cc_final: 0.7518 (tpt) REVERT: C 299 ARG cc_start: 0.8464 (tmt170) cc_final: 0.7366 (tpt170) REVERT: C 460 MET cc_start: 0.8419 (tpp) cc_final: 0.8184 (tpp) REVERT: C 560 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7554 (ptp90) REVERT: C 597 MET cc_start: 0.4300 (tpt) cc_final: 0.3554 (tpt) REVERT: C 780 MET cc_start: 0.8537 (tpp) cc_final: 0.8107 (tpp) outliers start: 55 outliers final: 37 residues processed: 176 average time/residue: 0.1605 time to fit residues: 41.5564 Evaluate side-chains 166 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 874 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 132 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 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 = 0.4183 r_free = 0.4183 target = 0.119394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.095653 restraints weight = 51363.057| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.70 r_work: 0.3541 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18081 Z= 0.188 Angle : 0.599 11.325 24680 Z= 0.306 Chirality : 0.043 0.183 2791 Planarity : 0.005 0.049 3195 Dihedral : 6.827 85.156 2574 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.27 % Favored : 91.69 % Rotamer: Outliers : 3.00 % Allowed : 19.06 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2249 helix: 0.71 (0.18), residues: 933 sheet: -1.60 (0.28), residues: 332 loop : -1.34 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 874 TYR 0.023 0.002 TYR A 696 PHE 0.029 0.002 PHE A 693 TRP 0.016 0.001 TRP A 337 HIS 0.006 0.001 HIS B 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (18080) covalent geometry : angle 0.59784 / 0.31 (24678) SS BOND : bond 0.00724 / 0.45 ( 1) SS BOND : angle 3.38818 / 1.47 ( 2) hydrogen bonds : bond 0.04335 / 3.06 ( 706) hydrogen bonds : angle 4.84767 / 3.44 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: A 354 LEU cc_start: 0.7383 (pp) cc_final: 0.6798 (mp) REVERT: A 478 GLU cc_start: 0.4009 (OUTLIER) cc_final: 0.3101 (tp30) REVERT: A 520 PHE cc_start: 0.7103 (t80) cc_final: 0.6592 (t80) REVERT: A 562 ARG cc_start: 0.6021 (tmt170) cc_final: 0.5775 (tmt170) REVERT: A 717 MET cc_start: 0.5488 (ptp) cc_final: 0.3010 (ppp) REVERT: A 773 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5544 (mpp) REVERT: A 794 MET cc_start: 0.4495 (mmp) cc_final: 0.4231 (mmm) REVERT: A 802 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6817 (mt) REVERT: A 848 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (pp) REVERT: A 850 MET cc_start: 0.8071 (pmm) cc_final: 0.7796 (pmm) REVERT: A 869 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 47 ARG cc_start: 0.7429 (mtp85) cc_final: 0.6852 (mtp85) REVERT: B 112 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6242 (mp-120) REVERT: B 135 LYS cc_start: 0.6931 (tppt) cc_final: 0.6624 (mmmm) REVERT: B 137 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6897 (mm-30) REVERT: B 163 MET cc_start: 0.8182 (tmm) cc_final: 0.7894 (tmm) REVERT: B 188 THR cc_start: 0.8521 (m) cc_final: 0.8293 (t) REVERT: B 217 PHE cc_start: 0.7339 (m-10) cc_final: 0.6960 (m-10) REVERT: B 467 ASN cc_start: 0.7929 (t0) cc_final: 0.7570 (t0) REVERT: B 610 THR cc_start: 0.5886 (OUTLIER) cc_final: 0.5685 (p) REVERT: C 113 MET cc_start: 0.7825 (tpt) cc_final: 0.7085 (tpt) REVERT: C 117 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7414 (mmt90) REVERT: C 131 LEU cc_start: 0.7482 (mt) cc_final: 0.7176 (mp) REVERT: C 158 MET cc_start: 0.7865 (tpt) cc_final: 0.7468 (tpt) REVERT: C 299 ARG cc_start: 0.8446 (tmt170) cc_final: 0.7325 (tpt170) REVERT: C 460 MET cc_start: 0.8437 (tpp) cc_final: 0.8197 (tpp) REVERT: C 560 ARG cc_start: 0.7903 (ptp90) cc_final: 0.7530 (ptp90) REVERT: C 597 MET cc_start: 0.4390 (tpt) cc_final: 0.3610 (tpt) REVERT: C 780 MET cc_start: 0.8607 (tpp) cc_final: 0.8154 (tpp) outliers start: 54 outliers final: 37 residues processed: 165 average time/residue: 0.1516 time to fit residues: 37.5927 Evaluate side-chains 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 874 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 126 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 192 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.119813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.096047 restraints weight = 51297.017| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.39 r_work: 0.3564 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18081 Z= 0.158 Angle : 0.580 9.934 24680 Z= 0.295 Chirality : 0.042 0.193 2791 Planarity : 0.005 0.047 3195 Dihedral : 6.778 84.747 2574 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.87 % Favored : 92.09 % Rotamer: Outliers : 3.11 % Allowed : 19.28 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2249 helix: 0.75 (0.18), residues: 934 sheet: -1.65 (0.29), residues: 316 loop : -1.35 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 255 TYR 0.021 0.001 TYR C 891 PHE 0.024 0.002 PHE C 300 TRP 0.012 0.001 TRP A 337 HIS 0.006 0.001 HIS B 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (18080) covalent geometry : angle 0.57878 / 0.29 (24678) SS BOND : bond 0.00662 / 0.41 ( 1) SS BOND : angle 4.82385 / 2.21 ( 2) hydrogen bonds : bond 0.04034 / 2.86 ( 706) hydrogen bonds : angle 4.77312 / 3.40 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 354 LEU cc_start: 0.7474 (pp) cc_final: 0.6933 (mp) REVERT: A 478 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.3024 (tp30) REVERT: A 548 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8168 (pp) REVERT: A 562 ARG cc_start: 0.6011 (tmt170) cc_final: 0.5786 (tmt170) REVERT: A 717 MET cc_start: 0.5488 (ptp) cc_final: 0.3744 (ppp) REVERT: A 794 MET cc_start: 0.4185 (mmp) cc_final: 0.3957 (mmm) REVERT: A 848 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 850 MET cc_start: 0.8068 (pmm) cc_final: 0.7782 (pmm) REVERT: A 869 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 47 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6817 (mtp85) REVERT: B 112 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6379 (mp-120) REVERT: B 135 LYS cc_start: 0.6969 (tppt) cc_final: 0.6653 (mmmm) REVERT: B 137 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6932 (mm-30) REVERT: B 163 MET cc_start: 0.8111 (tmm) cc_final: 0.7836 (tmm) REVERT: B 188 THR cc_start: 0.8500 (m) cc_final: 0.8273 (t) REVERT: B 217 PHE cc_start: 0.7432 (m-10) cc_final: 0.7062 (m-10) REVERT: B 467 ASN cc_start: 0.7430 (t0) cc_final: 0.7112 (t0) REVERT: B 610 THR cc_start: 0.5964 (OUTLIER) cc_final: 0.5760 (p) REVERT: C 113 MET cc_start: 0.7809 (tpt) cc_final: 0.7110 (tpt) REVERT: C 117 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7416 (mmt90) REVERT: C 131 LEU cc_start: 0.7514 (mt) cc_final: 0.7219 (mp) REVERT: C 158 MET cc_start: 0.7863 (tpt) cc_final: 0.7460 (tpt) REVERT: C 299 ARG cc_start: 0.8405 (tmt170) cc_final: 0.7331 (tpt170) REVERT: C 460 MET cc_start: 0.8406 (tpp) cc_final: 0.8175 (tpp) REVERT: C 560 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7490 (ptp90) REVERT: C 597 MET cc_start: 0.4485 (tpt) cc_final: 0.3688 (tpt) REVERT: C 780 MET cc_start: 0.8570 (tpp) cc_final: 0.8166 (tpp) outliers start: 56 outliers final: 43 residues processed: 169 average time/residue: 0.1494 time to fit residues: 38.0267 Evaluate side-chains 165 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 115 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 874 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 41 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 833 ASN ** C 128 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 = 0.4202 r_free = 0.4202 target = 0.120589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.097049 restraints weight = 51134.927| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.69 r_work: 0.3562 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18081 Z= 0.124 Angle : 0.560 10.872 24680 Z= 0.282 Chirality : 0.041 0.177 2791 Planarity : 0.004 0.047 3195 Dihedral : 6.687 83.956 2574 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.43 % Favored : 92.53 % Rotamer: Outliers : 2.67 % Allowed : 19.94 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2249 helix: 0.86 (0.18), residues: 937 sheet: -1.58 (0.29), residues: 315 loop : -1.31 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 440 TYR 0.019 0.001 TYR C 53 PHE 0.023 0.002 PHE C 300 TRP 0.012 0.001 TRP B 507 HIS 0.006 0.001 HIS B 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (18080) covalent geometry : angle 0.55980 / 0.28 (24678) SS BOND : bond 0.00404 / 0.25 ( 1) SS BOND : angle 3.15045 / 1.37 ( 2) hydrogen bonds : bond 0.03672 / 2.60 ( 706) hydrogen bonds : angle 4.63807 / 3.30 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.7429 (pp) cc_final: 0.7038 (mm) REVERT: A 478 GLU cc_start: 0.3839 (OUTLIER) cc_final: 0.2958 (tp30) REVERT: A 548 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 717 MET cc_start: 0.5502 (ptp) cc_final: 0.3868 (ppp) REVERT: A 794 MET cc_start: 0.4158 (mmp) cc_final: 0.3908 (mmm) REVERT: A 869 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8424 (mp) REVERT: B 47 ARG cc_start: 0.7417 (mtp85) cc_final: 0.6836 (mtp85) REVERT: B 112 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6341 (mp-120) REVERT: B 135 LYS cc_start: 0.7005 (tppt) cc_final: 0.6687 (mmmm) REVERT: B 137 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 163 MET cc_start: 0.8150 (tmm) cc_final: 0.7862 (tmm) REVERT: B 188 THR cc_start: 0.8482 (m) cc_final: 0.8264 (t) REVERT: B 217 PHE cc_start: 0.7440 (m-10) cc_final: 0.7067 (m-10) REVERT: B 467 ASN cc_start: 0.7259 (t0) cc_final: 0.6951 (t0) REVERT: B 610 THR cc_start: 0.5985 (OUTLIER) cc_final: 0.5770 (p) REVERT: C 113 MET cc_start: 0.7829 (tpt) cc_final: 0.7268 (tpt) REVERT: C 117 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7457 (mmt90) REVERT: C 158 MET cc_start: 0.7855 (tpt) cc_final: 0.7461 (tpt) REVERT: C 299 ARG cc_start: 0.8376 (tmt170) cc_final: 0.7320 (tpt170) REVERT: C 308 ARG cc_start: 0.5414 (mmm160) cc_final: 0.5201 (mtp85) REVERT: C 460 MET cc_start: 0.8429 (tpp) cc_final: 0.8174 (tpp) REVERT: C 560 ARG cc_start: 0.7896 (ptp90) cc_final: 0.7552 (ptp90) REVERT: C 597 MET cc_start: 0.4421 (tpt) cc_final: 0.3667 (tpt) REVERT: C 780 MET cc_start: 0.8558 (tpp) cc_final: 0.8192 (tpp) outliers start: 48 outliers final: 38 residues processed: 161 average time/residue: 0.1451 time to fit residues: 35.1443 Evaluate side-chains 159 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 824 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 51 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN ** C 128 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 = 0.4216 r_free = 0.4216 target = 0.121362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.094334 restraints weight = 51181.950| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.43 r_work: 0.3587 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18081 Z= 0.106 Angle : 0.557 16.721 24680 Z= 0.276 Chirality : 0.041 0.177 2791 Planarity : 0.004 0.047 3195 Dihedral : 6.589 83.405 2574 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 2.44 % Allowed : 20.11 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 2249 helix: 0.96 (0.18), residues: 944 sheet: -1.50 (0.29), residues: 317 loop : -1.28 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 90 TYR 0.016 0.001 TYR B 30 PHE 0.028 0.002 PHE C 363 TRP 0.013 0.001 TRP B 507 HIS 0.006 0.001 HIS B 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (18080) covalent geometry : angle 0.55669 / 0.28 (24678) SS BOND : bond 0.00446 / 0.28 ( 1) SS BOND : angle 2.29227 / 1.03 ( 2) hydrogen bonds : bond 0.03362 / 2.37 ( 706) hydrogen bonds : angle 4.53164 / 3.22 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4498 Ramachandran restraints generated. 2249 Oldfield, 0 Emsley, 2249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.7305 (pp) cc_final: 0.6917 (mm) REVERT: A 478 GLU cc_start: 0.3832 (OUTLIER) cc_final: 0.2960 (tp30) REVERT: A 717 MET cc_start: 0.5653 (ptp) cc_final: 0.5387 (pmm) REVERT: A 850 MET cc_start: 0.7959 (pmm) cc_final: 0.7696 (pmm) REVERT: A 869 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 47 ARG cc_start: 0.7326 (mtp85) cc_final: 0.6723 (mtp85) REVERT: B 112 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6314 (mp-120) REVERT: B 135 LYS cc_start: 0.6982 (tppt) cc_final: 0.6659 (mmmm) REVERT: B 137 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6993 (mm-30) REVERT: B 163 MET cc_start: 0.8166 (tmm) cc_final: 0.7866 (tmm) REVERT: B 188 THR cc_start: 0.8435 (m) cc_final: 0.8200 (t) REVERT: B 217 PHE cc_start: 0.7367 (m-10) cc_final: 0.7014 (m-10) REVERT: B 231 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 395 ASP cc_start: 0.7440 (m-30) cc_final: 0.7170 (p0) REVERT: B 467 ASN cc_start: 0.7201 (t0) cc_final: 0.6935 (t0) REVERT: B 480 MET cc_start: 0.6847 (mmm) cc_final: 0.6213 (mmm) REVERT: B 610 THR cc_start: 0.5831 (OUTLIER) cc_final: 0.5618 (p) REVERT: C 113 MET cc_start: 0.7824 (tpt) cc_final: 0.7155 (tpt) REVERT: C 117 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7400 (mmt90) REVERT: C 131 LEU cc_start: 0.7439 (mt) cc_final: 0.7226 (mp) REVERT: C 158 MET cc_start: 0.7826 (tpt) cc_final: 0.7461 (tpt) REVERT: C 299 ARG cc_start: 0.8351 (tmt170) cc_final: 0.7293 (tpt170) REVERT: C 460 MET cc_start: 0.8408 (tpp) cc_final: 0.8151 (tpp) REVERT: C 560 ARG cc_start: 0.7861 (ptp90) cc_final: 0.7523 (ptp90) REVERT: C 597 MET cc_start: 0.4404 (tpt) cc_final: 0.3657 (tpt) REVERT: C 780 MET cc_start: 0.8472 (tpp) cc_final: 0.8130 (tpp) outliers start: 44 outliers final: 34 residues processed: 159 average time/residue: 0.1525 time to fit residues: 35.8493 Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 824 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 61 optimal weight: 0.0270 chunk 32 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 223 optimal weight: 0.0000 chunk 92 optimal weight: 0.9990 overall best weight: 0.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.094505 restraints weight = 51274.582| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.12 r_work: 0.3622 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18081 Z= 0.103 Angle : 0.561 17.105 24680 Z= 0.275 Chirality : 0.041 0.175 2791 Planarity : 0.004 0.049 3195 Dihedral : 6.518 83.359 2573 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.24 % Rotamer: Outliers : 2.33 % Allowed : 20.17 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 2249 helix: 1.10 (0.18), residues: 936 sheet: -1.50 (0.30), residues: 307 loop : -1.24 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 90 TYR 0.016 0.001 TYR C 53 PHE 0.028 0.001 PHE C 363 TRP 0.011 0.001 TRP B 507 HIS 0.006 0.001 HIS B 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (18080) covalent geometry : angle 0.56057 / 0.27 (24678) SS BOND : bond 0.00382 / 0.24 ( 1) SS BOND : angle 2.04279 / 0.92 ( 2) hydrogen bonds : bond 0.03189 / 2.25 ( 706) hydrogen bonds : angle 4.44456 / 3.16 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.29 seconds wall clock time: 79 minutes 48.10 seconds (4788.10 seconds total)