Starting phenix.real_space_refine on Mon Sep 30 05:56:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/09_2024/7tjk_25928.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/09_2024/7tjk_25928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/09_2024/7tjk_25928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/09_2024/7tjk_25928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/09_2024/7tjk_25928.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjk_25928/09_2024/7tjk_25928.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 93 5.49 5 Mg 4 5.21 5 S 107 5.16 5 C 15504 2.51 5 N 4101 2.21 5 O 4859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24668 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3889 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 475} Chain breaks: 4 Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2057 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4504 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 528} Chain breaks: 5 Chain: "D" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3536 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 3588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3588 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2163 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain breaks: 2 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2995 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 13.69, per 1000 atoms: 0.55 Number of scatterers: 24668 At special positions: 0 Unit cell: (116.96, 138.46, 179.74, 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 107 16.00 P 93 15.00 Mg 4 11.99 O 4859 8.00 N 4101 7.00 C 15504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.58 Conformation dependent library (CDL) restraints added in 2.7 seconds 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5406 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 13 sheets defined 62.3% alpha, 7.8% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 7.95 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.513A pdb=" N LYS A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 378 " --> pdb=" O PHE A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.582A pdb=" N LEU A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.927A pdb=" N GLY A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 4.256A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 484 through 502 removed outlier: 3.520A pdb=" N GLN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.522A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.693A pdb=" N VAL A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.532A pdb=" N LYS A 558 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 removed outlier: 3.529A pdb=" N VAL A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.962A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 702 through 726 Processing helix chain 'A' and resid 774 through 785 removed outlier: 3.567A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.379A pdb=" N THR A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 815 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.529A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 5.100A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.549A pdb=" N ALA A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.916A pdb=" N ASN A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.597A pdb=" N LYS B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.718A pdb=" N ARG B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.508A pdb=" N LYS B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.953A pdb=" N LYS B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.515A pdb=" N ASP B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 447 removed outlier: 4.004A pdb=" N ILE B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.876A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 50 through 93 removed outlier: 3.816A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.609A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 229 removed outlier: 3.546A pdb=" N TYR C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.988A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 295 through 308 removed outlier: 3.549A pdb=" N ASN C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 332 removed outlier: 3.679A pdb=" N LEU C 316 " --> pdb=" O HIS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.904A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Proline residue: C 340 - end of helix removed outlier: 4.080A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 401 through 416 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 474 through 479 removed outlier: 3.686A pdb=" N ILE C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 512 through 516 removed outlier: 3.561A pdb=" N LYS C 515 " --> pdb=" O ASP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.855A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 Processing helix chain 'C' and resid 549 through 558 Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 574 through 595 removed outlier: 3.856A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.525A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.778A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.285A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.748A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.640A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 361 through 372 removed outlier: 3.560A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.628A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.542A pdb=" N ASN D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.520A pdb=" N MET D 496 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.549A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.630A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.868A pdb=" N GLN D 528 " --> pdb=" O SER D 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.536A pdb=" N ILE E 28 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 29' Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.556A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 89 removed outlier: 3.739A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.621A pdb=" N LYS E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.548A pdb=" N LEU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 193 through 211 removed outlier: 5.740A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.602A pdb=" N ILE E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 252 removed outlier: 5.671A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 271 removed outlier: 3.579A pdb=" N LEU E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 280 through 288 removed outlier: 3.716A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.814A pdb=" N LEU E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 345 through 350 removed outlier: 3.786A pdb=" N ILE E 349 " --> pdb=" O TYR E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.575A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 removed outlier: 3.610A pdb=" N ILE E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 15 Processing helix chain 'F' and resid 26 through 47 removed outlier: 4.194A pdb=" N ASN F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 56 removed outlier: 3.890A pdb=" N VAL F 55 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.779A pdb=" N ILE F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.787A pdb=" N SER F 83 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 281 through 290 removed outlier: 3.563A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 295 through 309 removed outlier: 3.729A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.594A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.824A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER F 348 " --> pdb=" O HIS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 371 removed outlier: 4.313A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 387 Processing helix chain 'F' and resid 393 through 402 removed outlier: 4.042A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 Processing helix chain 'I' and resid 54 through 62 Processing helix chain 'I' and resid 81 through 99 removed outlier: 3.601A pdb=" N GLU I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 126 removed outlier: 3.530A pdb=" N PHE I 126 " --> pdb=" O ILE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 180 through 188 Processing helix chain 'I' and resid 201 through 210 removed outlier: 4.061A pdb=" N LEU I 205 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 229 removed outlier: 3.551A pdb=" N LEU I 229 " --> pdb=" O ASP I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 248 removed outlier: 4.604A pdb=" N THR I 241 " --> pdb=" O GLN I 237 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE I 242 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU I 244 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU I 248 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'I' and resid 292 through 304 Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'I' and resid 330 through 349 Processing helix chain 'I' and resid 386 through 397 removed outlier: 3.728A pdb=" N ILE I 390 " --> pdb=" O GLY I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 Processing helix chain 'I' and resid 411 through 428 removed outlier: 3.800A pdb=" N LEU I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN I 428 " --> pdb=" O SER I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 446 removed outlier: 3.811A pdb=" N LYS I 442 " --> pdb=" O ASP I 438 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS I 446 " --> pdb=" O LYS I 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 468 Processing helix chain 'I' and resid 494 through 504 removed outlier: 3.580A pdb=" N TYR I 499 " --> pdb=" O MET I 495 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 500 " --> pdb=" O ARG I 496 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS I 504 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 512 removed outlier: 3.603A pdb=" N LEU I 512 " --> pdb=" O LYS I 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.332A pdb=" N LEU A 509 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A 564 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 511 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASP A 566 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 513 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA A 478 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 657 through 659 Processing sheet with id=AA3, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.299A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.479A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE C 240 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 107 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.823A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 133 Processing sheet with id=AA9, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 62 removed outlier: 4.435A pdb=" N HIS E 58 " --> pdb=" O CYS E 127 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU E 33 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N MET E 170 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL E 187 " --> pdb=" O ASN E 32 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE E 189 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN E 36 " --> pdb=" O PHE E 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AB3, first strand: chain 'I' and resid 152 through 154 removed outlier: 8.537A pdb=" N VAL I 219 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA I 166 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL I 221 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR I 168 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP I 223 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE I 170 " --> pdb=" O ASP I 223 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE I 218 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE I 259 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL I 220 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N MET I 261 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 222 " --> pdb=" O MET I 261 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASN I 263 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY I 108 " --> pdb=" O ALA I 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 471 through 477 1129 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3832 1.31 - 1.44: 7010 1.44 - 1.56: 13980 1.56 - 1.69: 183 1.69 - 1.82: 176 Bond restraints: 25181 Sorted by residual: bond pdb=" N ILE I 170 " pdb=" CA ILE I 170 " ideal model delta sigma weight residual 1.459 1.518 -0.059 1.15e-02 7.56e+03 2.65e+01 bond pdb=" N ASN I 171 " pdb=" CA ASN I 171 " ideal model delta sigma weight residual 1.456 1.518 -0.063 1.22e-02 6.72e+03 2.64e+01 bond pdb=" C LYS B 419 " pdb=" O LYS B 419 " ideal model delta sigma weight residual 1.236 1.183 0.052 1.31e-02 5.83e+03 1.60e+01 bond pdb=" C ASN I 171 " pdb=" O ASN I 171 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" C MET A 779 " pdb=" O MET A 779 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.29e-02 6.01e+03 1.21e+01 ... (remaining 25176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 34186 4.23 - 8.45: 175 8.45 - 12.68: 12 12.68 - 16.91: 0 16.91 - 21.13: 1 Bond angle restraints: 34374 Sorted by residual: angle pdb=" PB ATP I1001 " pdb=" O3B ATP I1001 " pdb=" PG ATP I1001 " ideal model delta sigma weight residual 139.87 131.07 8.80 1.00e+00 1.00e+00 7.74e+01 angle pdb=" PA ATP I1001 " pdb=" O3A ATP I1001 " pdb=" PB ATP I1001 " ideal model delta sigma weight residual 136.83 129.57 7.26 1.00e+00 1.00e+00 5.28e+01 angle pdb=" N GLU D 151 " pdb=" CA GLU D 151 " pdb=" CB GLU D 151 " ideal model delta sigma weight residual 110.16 119.19 -9.03 1.48e+00 4.57e-01 3.72e+01 angle pdb=" N ASN I 171 " pdb=" CA ASN I 171 " pdb=" CB ASN I 171 " ideal model delta sigma weight residual 109.97 118.11 -8.14 1.47e+00 4.63e-01 3.07e+01 angle pdb=" C ILE F 81 " pdb=" N ASP F 82 " pdb=" CA ASP F 82 " ideal model delta sigma weight residual 120.38 127.29 -6.91 1.46e+00 4.69e-01 2.24e+01 ... (remaining 34369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13139 17.97 - 35.93: 1383 35.93 - 53.90: 499 53.90 - 71.87: 121 71.87 - 89.84: 29 Dihedral angle restraints: 15171 sinusoidal: 6901 harmonic: 8270 Sorted by residual: dihedral pdb=" CA SER A 854 " pdb=" C SER A 854 " pdb=" N ASP A 855 " pdb=" CA ASP A 855 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 15168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3159 0.061 - 0.122: 666 0.122 - 0.183: 78 0.183 - 0.245: 9 0.245 - 0.306: 2 Chirality restraints: 3914 Sorted by residual: chirality pdb=" CB VAL B 384 " pdb=" CA VAL B 384 " pdb=" CG1 VAL B 384 " pdb=" CG2 VAL B 384 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG I 240 " pdb=" N ARG I 240 " pdb=" C ARG I 240 " pdb=" CB ARG I 240 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA TRP C 494 " pdb=" N TRP C 494 " pdb=" C TRP C 494 " pdb=" CB TRP C 494 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3911 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 26 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 27 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 50 " -0.021 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C LYS F 50 " 0.075 2.00e-02 2.50e+03 pdb=" O LYS F 50 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN F 51 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 418 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ILE B 418 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE B 418 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 419 " 0.020 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 131 2.49 - 3.09: 15690 3.09 - 3.69: 38873 3.69 - 4.30: 58906 4.30 - 4.90: 92302 Nonbonded interactions: 205902 Sorted by model distance: nonbonded pdb=" OD1 ASP E 136 " pdb=" O HOH E1101 " model vdw 1.886 3.040 nonbonded pdb=" O2B ATP I1001 " pdb="MG MG I1002 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR I 115 " pdb="MG MG I1002 " model vdw 2.082 2.170 nonbonded pdb=" O2G ATP D1001 " pdb="MG MG D1002 " model vdw 2.108 2.170 ... (remaining 205897 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: 4.080 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: 0.000 Extract box with map and model: 2.690 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.410 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 25181 Z= 0.295 Angle : 0.885 21.133 34374 Z= 0.509 Chirality : 0.050 0.306 3914 Planarity : 0.007 0.122 4013 Dihedral : 17.378 89.836 9765 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.39 % Allowed : 0.47 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 2721 helix: -1.13 (0.11), residues: 1523 sheet: 0.39 (0.31), residues: 253 loop : -1.05 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 450 HIS 0.012 0.002 HIS C 65 PHE 0.042 0.002 PHE F 329 TYR 0.026 0.002 TYR F 80 ARG 0.005 0.001 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 519 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8163 (mptp) REVERT: A 544 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 343 VAL cc_start: 0.8379 (m) cc_final: 0.8042 (p) REVERT: C 395 PHE cc_start: 0.6935 (m-80) cc_final: 0.6231 (m-80) REVERT: C 408 PHE cc_start: 0.8881 (t80) cc_final: 0.8631 (t80) REVERT: D 83 ASP cc_start: 0.7777 (t0) cc_final: 0.7537 (t70) REVERT: F 67 GLN cc_start: 0.8279 (tt0) cc_final: 0.7872 (tt0) REVERT: F 100 GLN cc_start: 0.8607 (mt0) cc_final: 0.8404 (mt0) REVERT: F 332 PHE cc_start: 0.7911 (m-10) cc_final: 0.7455 (m-10) REVERT: F 417 GLN cc_start: 0.8649 (tt0) cc_final: 0.7896 (mm-40) REVERT: I 200 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8013 (pptt) REVERT: I 247 LEU cc_start: 0.8453 (tt) cc_final: 0.8174 (mt) REVERT: I 409 LYS cc_start: 0.8950 (mttt) cc_final: 0.8713 (mtpp) REVERT: I 426 LYS cc_start: 0.8287 (mttt) cc_final: 0.7995 (mtmm) outliers start: 10 outliers final: 5 residues processed: 525 average time/residue: 1.6500 time to fit residues: 973.9214 Evaluate side-chains 282 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 502 GLN A 810 ASN C 38 HIS C 477 GLN D 158 HIS D 323 HIS ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 HIS F 7 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN F 410 ASN I 99 HIS I 151 ASN I 203 GLN I 232 ASN I 327 ASN I 454 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 25181 Z= 0.415 Angle : 0.664 14.220 34374 Z= 0.354 Chirality : 0.045 0.247 3914 Planarity : 0.005 0.057 4013 Dihedral : 17.943 86.273 4080 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.38 % Allowed : 10.66 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2721 helix: 0.36 (0.13), residues: 1554 sheet: 0.26 (0.30), residues: 254 loop : -0.68 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 456 HIS 0.008 0.001 HIS F 59 PHE 0.024 0.002 PHE F 332 TYR 0.029 0.002 TYR C 483 ARG 0.011 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 292 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8305 (mptp) REVERT: A 502 GLN cc_start: 0.8641 (pt0) cc_final: 0.8426 (pt0) REVERT: A 678 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7299 (ttp80) REVERT: B 268 ASP cc_start: 0.7980 (t70) cc_final: 0.7759 (m-30) REVERT: B 377 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8203 (mppt) REVERT: C 80 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: C 147 MET cc_start: 0.8973 (mmp) cc_final: 0.8697 (mmp) REVERT: C 343 VAL cc_start: 0.8432 (m) cc_final: 0.8153 (p) REVERT: C 356 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7603 (ttp-110) REVERT: C 391 PHE cc_start: 0.7694 (t80) cc_final: 0.7320 (t80) REVERT: C 395 PHE cc_start: 0.7351 (m-80) cc_final: 0.7142 (m-80) REVERT: C 408 PHE cc_start: 0.8929 (t80) cc_final: 0.7949 (t80) REVERT: C 411 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7971 (ptt180) REVERT: C 461 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8173 (tt) REVERT: D 295 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6952 (mpt-90) REVERT: D 467 ASP cc_start: 0.8048 (t0) cc_final: 0.7830 (t0) REVERT: E 170 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7801 (mmm) REVERT: E 188 MET cc_start: 0.8640 (mpt) cc_final: 0.8269 (mpt) REVERT: E 275 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5878 (mmtm) REVERT: E 367 LYS cc_start: 0.8457 (pptt) cc_final: 0.8060 (pttp) REVERT: F 5 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8424 (tp40) REVERT: F 100 GLN cc_start: 0.8791 (mt0) cc_final: 0.8541 (mt0) REVERT: F 354 MET cc_start: 0.6010 (mmp) cc_final: 0.5775 (tpt) REVERT: F 417 GLN cc_start: 0.8777 (tt0) cc_final: 0.7946 (mm-40) REVERT: I 57 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8036 (mtm180) REVERT: I 200 LYS cc_start: 0.8477 (ptpp) cc_final: 0.8250 (pptt) outliers start: 61 outliers final: 23 residues processed: 327 average time/residue: 1.4261 time to fit residues: 534.2242 Evaluate side-chains 279 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 496 ARG Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN C 69 HIS E 2 ASN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25181 Z= 0.198 Angle : 0.540 13.963 34374 Z= 0.289 Chirality : 0.041 0.253 3914 Planarity : 0.004 0.050 4013 Dihedral : 17.689 87.707 4073 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.11 % Allowed : 13.04 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2721 helix: 1.01 (0.13), residues: 1554 sheet: 0.26 (0.31), residues: 252 loop : -0.55 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 456 HIS 0.008 0.001 HIS F 8 PHE 0.016 0.001 PHE C 455 TYR 0.019 0.001 TYR C 483 ARG 0.010 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 265 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7211 (ttp80) REVERT: A 681 ARG cc_start: 0.8195 (tmm-80) cc_final: 0.7991 (tmm-80) REVERT: B 268 ASP cc_start: 0.7910 (t70) cc_final: 0.7641 (m-30) REVERT: B 377 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8184 (mppt) REVERT: C 80 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: C 343 VAL cc_start: 0.8375 (m) cc_final: 0.8114 (p) REVERT: C 391 PHE cc_start: 0.7588 (t80) cc_final: 0.7312 (t80) REVERT: C 395 PHE cc_start: 0.7515 (m-80) cc_final: 0.7122 (m-80) REVERT: C 408 PHE cc_start: 0.8865 (t80) cc_final: 0.8470 (t80) REVERT: C 411 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7969 (ptt180) REVERT: C 412 PHE cc_start: 0.8601 (t80) cc_final: 0.8390 (t80) REVERT: D 258 GLU cc_start: 0.8225 (mp0) cc_final: 0.8024 (mp0) REVERT: D 295 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6927 (mpt180) REVERT: D 467 ASP cc_start: 0.8019 (t0) cc_final: 0.7790 (t0) REVERT: E 188 MET cc_start: 0.8690 (mpt) cc_final: 0.8359 (mpt) REVERT: E 275 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5844 (mmtm) REVERT: E 367 LYS cc_start: 0.8452 (pptt) cc_final: 0.8064 (pttp) REVERT: F 5 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8423 (tp40) REVERT: F 100 GLN cc_start: 0.8659 (mt0) cc_final: 0.8409 (mt0) REVERT: F 277 TYR cc_start: 0.7560 (m-80) cc_final: 0.7327 (m-80) REVERT: F 318 GLN cc_start: 0.6404 (mt0) cc_final: 0.5858 (mt0) REVERT: F 321 CYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7479 (p) REVERT: F 354 MET cc_start: 0.6026 (mmp) cc_final: 0.5775 (tpt) REVERT: F 417 GLN cc_start: 0.8784 (tt0) cc_final: 0.7985 (mm110) REVERT: I 57 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7913 (mtm180) REVERT: I 89 MET cc_start: 0.8307 (mmm) cc_final: 0.8065 (mmt) REVERT: I 200 LYS cc_start: 0.8439 (ptpp) cc_final: 0.8186 (pptt) REVERT: I 247 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8555 (mt) REVERT: I 502 MET cc_start: 0.8904 (mmt) cc_final: 0.8605 (mmt) outliers start: 54 outliers final: 20 residues processed: 296 average time/residue: 1.4662 time to fit residues: 496.3613 Evaluate side-chains 264 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 254 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 273 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN C 430 ASN E 91 ASN E 245 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 67 GLN I 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25181 Z= 0.290 Angle : 0.570 13.854 34374 Z= 0.303 Chirality : 0.042 0.253 3914 Planarity : 0.004 0.052 4013 Dihedral : 17.701 86.179 4071 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.58 % Allowed : 13.58 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2721 helix: 1.22 (0.14), residues: 1563 sheet: 0.17 (0.30), residues: 252 loop : -0.49 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 539 HIS 0.006 0.001 HIS F 59 PHE 0.018 0.001 PHE D 363 TYR 0.022 0.001 TYR C 483 ARG 0.012 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 251 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7328 (mp0) cc_final: 0.7112 (mt-10) REVERT: A 647 PHE cc_start: 0.8652 (m-80) cc_final: 0.8055 (m-80) REVERT: A 678 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7337 (ttp80) REVERT: B 377 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8142 (mppt) REVERT: C 80 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: C 343 VAL cc_start: 0.8342 (m) cc_final: 0.8063 (p) REVERT: C 391 PHE cc_start: 0.7575 (t80) cc_final: 0.7303 (t80) REVERT: C 395 PHE cc_start: 0.7411 (m-80) cc_final: 0.7025 (m-80) REVERT: C 408 PHE cc_start: 0.8878 (t80) cc_final: 0.8502 (t80) REVERT: C 411 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8054 (ptt180) REVERT: C 585 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6538 (tpt) REVERT: D 295 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6900 (mpt180) REVERT: D 467 ASP cc_start: 0.8047 (t0) cc_final: 0.7794 (t0) REVERT: E 170 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: E 188 MET cc_start: 0.8764 (mpt) cc_final: 0.8327 (mpt) REVERT: E 275 LYS cc_start: 0.6353 (OUTLIER) cc_final: 0.5861 (mmtm) REVERT: E 367 LYS cc_start: 0.8510 (pptt) cc_final: 0.8104 (pttp) REVERT: E 449 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7208 (mtp85) REVERT: F 5 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8369 (tp40) REVERT: F 277 TYR cc_start: 0.7796 (m-80) cc_final: 0.7566 (m-80) REVERT: F 287 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7961 (mmp80) REVERT: F 318 GLN cc_start: 0.6464 (mt0) cc_final: 0.5938 (mt0) REVERT: F 321 CYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7404 (p) REVERT: F 354 MET cc_start: 0.6021 (mmp) cc_final: 0.5680 (tpt) REVERT: F 417 GLN cc_start: 0.8781 (tt0) cc_final: 0.8007 (mm110) REVERT: I 57 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8045 (mtm180) REVERT: I 200 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8153 (pptt) REVERT: I 247 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8641 (mt) REVERT: I 502 MET cc_start: 0.8916 (mmt) cc_final: 0.8659 (mmt) outliers start: 66 outliers final: 26 residues processed: 288 average time/residue: 1.4290 time to fit residues: 470.4411 Evaluate side-chains 270 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 233 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN D 58 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 25181 Z= 0.475 Angle : 0.650 12.987 34374 Z= 0.342 Chirality : 0.046 0.242 3914 Planarity : 0.004 0.052 4013 Dihedral : 17.936 86.120 4071 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.97 % Allowed : 14.25 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2721 helix: 1.10 (0.13), residues: 1560 sheet: 0.04 (0.31), residues: 247 loop : -0.48 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 539 HIS 0.006 0.001 HIS F 59 PHE 0.021 0.002 PHE D 363 TYR 0.026 0.002 TYR C 483 ARG 0.014 0.001 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 249 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 GLU cc_start: 0.8221 (mp0) cc_final: 0.7899 (mp0) REVERT: A 647 PHE cc_start: 0.8609 (m-80) cc_final: 0.8239 (m-80) REVERT: A 678 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7440 (ttp80) REVERT: A 813 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8293 (ttmm) REVERT: A 849 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9398 (mp) REVERT: B 377 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8195 (mppt) REVERT: C 80 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 391 PHE cc_start: 0.7563 (t80) cc_final: 0.7362 (t80) REVERT: C 395 PHE cc_start: 0.7509 (m-80) cc_final: 0.6851 (m-80) REVERT: C 408 PHE cc_start: 0.8903 (t80) cc_final: 0.8641 (t80) REVERT: C 577 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7436 (t70) REVERT: D 295 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6871 (mpt180) REVERT: D 467 ASP cc_start: 0.8068 (t0) cc_final: 0.7811 (t0) REVERT: E 188 MET cc_start: 0.8795 (mpt) cc_final: 0.8287 (mpt) REVERT: E 275 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5688 (mmmm) REVERT: E 367 LYS cc_start: 0.8613 (pptt) cc_final: 0.8213 (tmmm) REVERT: E 449 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7255 (mtp85) REVERT: F 5 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8495 (tp40) REVERT: F 30 LYS cc_start: 0.7919 (ptpp) cc_final: 0.7709 (pttm) REVERT: F 67 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: F 71 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: F 100 GLN cc_start: 0.8796 (mt0) cc_final: 0.8579 (mt0) REVERT: F 277 TYR cc_start: 0.7871 (m-80) cc_final: 0.7615 (m-80) REVERT: F 287 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (mmp80) REVERT: F 354 MET cc_start: 0.6126 (mmp) cc_final: 0.5703 (tpt) REVERT: F 417 GLN cc_start: 0.8777 (tt0) cc_final: 0.7972 (mm-40) REVERT: I 57 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8069 (mtm180) REVERT: I 200 LYS cc_start: 0.8486 (ptpp) cc_final: 0.8162 (ptmt) REVERT: I 206 GLN cc_start: 0.8919 (tt0) cc_final: 0.8396 (pt0) outliers start: 76 outliers final: 29 residues processed: 298 average time/residue: 1.5066 time to fit residues: 511.9462 Evaluate side-chains 275 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN C 400 ASN D 58 GLN D 152 GLN F 7 GLN F 67 GLN F 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25181 Z= 0.183 Angle : 0.543 13.503 34374 Z= 0.287 Chirality : 0.040 0.281 3914 Planarity : 0.003 0.059 4013 Dihedral : 17.672 87.224 4071 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.22 % Allowed : 15.61 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2721 helix: 1.43 (0.14), residues: 1561 sheet: 0.05 (0.31), residues: 247 loop : -0.34 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 154 HIS 0.004 0.001 HIS C 69 PHE 0.012 0.001 PHE D 363 TYR 0.017 0.001 TYR C 483 ARG 0.015 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 256 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7392 (mp0) cc_final: 0.7172 (mt-10) REVERT: A 606 GLU cc_start: 0.8191 (mp0) cc_final: 0.7899 (mp0) REVERT: A 678 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7403 (ttp80) REVERT: B 377 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8191 (mppt) REVERT: C 80 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: C 343 VAL cc_start: 0.8369 (m) cc_final: 0.8042 (p) REVERT: C 395 PHE cc_start: 0.7522 (m-80) cc_final: 0.6796 (m-80) REVERT: C 577 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7461 (t70) REVERT: C 585 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6524 (tpt) REVERT: D 295 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6813 (mpt180) REVERT: D 467 ASP cc_start: 0.8048 (t0) cc_final: 0.7795 (t0) REVERT: E 188 MET cc_start: 0.8768 (mpt) cc_final: 0.8386 (mpt) REVERT: E 367 LYS cc_start: 0.8647 (pptt) cc_final: 0.8270 (pttp) REVERT: F 5 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8367 (tp40) REVERT: F 67 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: F 71 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: F 277 TYR cc_start: 0.7866 (m-80) cc_final: 0.7424 (m-80) REVERT: F 279 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7375 (tppt) REVERT: F 280 MET cc_start: 0.5684 (mtp) cc_final: 0.5289 (mtt) REVERT: F 318 GLN cc_start: 0.6435 (mt0) cc_final: 0.5906 (mt0) REVERT: F 321 CYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7477 (p) REVERT: F 351 CYS cc_start: 0.7677 (m) cc_final: 0.7407 (m) REVERT: F 354 MET cc_start: 0.6221 (mmp) cc_final: 0.5776 (tpt) REVERT: F 417 GLN cc_start: 0.8771 (tt0) cc_final: 0.7956 (mm-40) REVERT: F 424 ARG cc_start: 0.7412 (mmp80) cc_final: 0.7199 (mpt-90) REVERT: I 200 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8223 (ptmt) REVERT: I 206 GLN cc_start: 0.8889 (tt0) cc_final: 0.8367 (pt0) REVERT: I 261 MET cc_start: 0.7837 (mtm) cc_final: 0.7587 (mtt) outliers start: 57 outliers final: 21 residues processed: 293 average time/residue: 1.4240 time to fit residues: 477.9489 Evaluate side-chains 261 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 600 ASN C 400 ASN F 7 GLN F 67 GLN F 73 HIS I 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25181 Z= 0.239 Angle : 0.563 13.456 34374 Z= 0.296 Chirality : 0.041 0.271 3914 Planarity : 0.003 0.069 4013 Dihedral : 17.634 86.682 4071 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.38 % Allowed : 15.89 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2721 helix: 1.48 (0.14), residues: 1561 sheet: 0.07 (0.31), residues: 247 loop : -0.31 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 154 HIS 0.005 0.001 HIS F 73 PHE 0.031 0.001 PHE C 391 TYR 0.019 0.001 TYR C 483 ARG 0.017 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 249 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 GLU cc_start: 0.8219 (mp0) cc_final: 0.7926 (mp0) REVERT: A 678 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7409 (ttp80) REVERT: B 377 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8166 (mppt) REVERT: C 80 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: C 343 VAL cc_start: 0.8349 (m) cc_final: 0.8042 (p) REVERT: C 395 PHE cc_start: 0.7528 (m-80) cc_final: 0.7075 (m-80) REVERT: C 577 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7223 (t0) REVERT: C 585 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6517 (tpt) REVERT: D 295 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6808 (mpt180) REVERT: D 467 ASP cc_start: 0.8046 (t0) cc_final: 0.7804 (t0) REVERT: E 188 MET cc_start: 0.8797 (mpt) cc_final: 0.8343 (mpt) REVERT: E 357 ILE cc_start: 0.7929 (mm) cc_final: 0.7596 (mm) REVERT: E 367 LYS cc_start: 0.8680 (pptt) cc_final: 0.8304 (pttp) REVERT: E 449 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7256 (mtp85) REVERT: F 5 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8368 (tp40) REVERT: F 67 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: F 71 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: F 100 GLN cc_start: 0.8829 (mt0) cc_final: 0.8621 (mt0) REVERT: F 277 TYR cc_start: 0.7829 (m-80) cc_final: 0.7438 (m-80) REVERT: F 279 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7467 (tppt) REVERT: F 318 GLN cc_start: 0.6484 (mt0) cc_final: 0.5958 (mt0) REVERT: F 321 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7498 (p) REVERT: F 354 MET cc_start: 0.6317 (mmp) cc_final: 0.5864 (tpt) REVERT: F 417 GLN cc_start: 0.8796 (tt0) cc_final: 0.8031 (mm110) REVERT: F 424 ARG cc_start: 0.7525 (mmp80) cc_final: 0.7183 (tpp-160) REVERT: I 200 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8211 (ptmt) REVERT: I 206 GLN cc_start: 0.8932 (tt0) cc_final: 0.8399 (pt0) REVERT: I 247 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8551 (mt) REVERT: I 502 MET cc_start: 0.8908 (mmt) cc_final: 0.8643 (mmt) outliers start: 61 outliers final: 29 residues processed: 290 average time/residue: 1.4151 time to fit residues: 472.5548 Evaluate side-chains 275 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 52 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN F 7 GLN F 67 GLN F 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25181 Z= 0.213 Angle : 0.563 14.067 34374 Z= 0.294 Chirality : 0.041 0.283 3914 Planarity : 0.003 0.075 4013 Dihedral : 17.581 86.913 4071 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.95 % Allowed : 16.63 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2721 helix: 1.54 (0.14), residues: 1561 sheet: 0.07 (0.31), residues: 247 loop : -0.27 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 154 HIS 0.004 0.001 HIS C 69 PHE 0.014 0.001 PHE F 292 TYR 0.018 0.001 TYR C 483 ARG 0.017 0.000 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 252 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 GLU cc_start: 0.8226 (mp0) cc_final: 0.7945 (mp0) REVERT: A 678 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7410 (ttp80) REVERT: B 377 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8164 (mppt) REVERT: C 80 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: C 343 VAL cc_start: 0.8363 (m) cc_final: 0.8042 (p) REVERT: C 391 PHE cc_start: 0.7746 (t80) cc_final: 0.7253 (t80) REVERT: C 395 PHE cc_start: 0.7410 (m-80) cc_final: 0.7143 (m-80) REVERT: C 577 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7223 (t0) REVERT: C 585 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6492 (tpt) REVERT: D 295 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6817 (mpt180) REVERT: D 467 ASP cc_start: 0.8055 (t0) cc_final: 0.7809 (t0) REVERT: E 188 MET cc_start: 0.8795 (mpt) cc_final: 0.8353 (mpt) REVERT: E 357 ILE cc_start: 0.7941 (mm) cc_final: 0.7608 (mm) REVERT: E 367 LYS cc_start: 0.8681 (pptt) cc_final: 0.8246 (tmmm) REVERT: E 437 MET cc_start: 0.7481 (tpp) cc_final: 0.7205 (tpt) REVERT: E 449 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7221 (mtp85) REVERT: F 5 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8317 (tp40) REVERT: F 67 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: F 71 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: F 80 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: F 277 TYR cc_start: 0.7875 (m-80) cc_final: 0.7494 (m-80) REVERT: F 279 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7523 (tppt) REVERT: F 318 GLN cc_start: 0.6483 (mt0) cc_final: 0.5940 (mt0) REVERT: F 321 CYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7442 (p) REVERT: F 354 MET cc_start: 0.6201 (mmp) cc_final: 0.5838 (tpt) REVERT: F 417 GLN cc_start: 0.8798 (tt0) cc_final: 0.8033 (mm110) REVERT: F 424 ARG cc_start: 0.7468 (mmp80) cc_final: 0.7202 (tpp-160) REVERT: I 200 LYS cc_start: 0.8454 (ptpp) cc_final: 0.8203 (ptmt) REVERT: I 206 GLN cc_start: 0.8959 (tt0) cc_final: 0.8435 (pt0) REVERT: I 247 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8546 (mt) REVERT: I 502 MET cc_start: 0.8910 (mmt) cc_final: 0.8577 (mmt) outliers start: 50 outliers final: 33 residues processed: 288 average time/residue: 1.3738 time to fit residues: 455.9684 Evaluate side-chains 280 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 236 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 240 optimal weight: 7.9990 chunk 253 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 600 ASN A 608 GLN F 7 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 73 HIS I 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25181 Z= 0.355 Angle : 0.617 14.288 34374 Z= 0.322 Chirality : 0.044 0.265 3914 Planarity : 0.004 0.077 4013 Dihedral : 17.719 86.396 4071 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.22 % Allowed : 16.47 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2721 helix: 1.45 (0.14), residues: 1553 sheet: 0.06 (0.31), residues: 247 loop : -0.28 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 154 HIS 0.004 0.001 HIS A 629 PHE 0.018 0.001 PHE D 363 TYR 0.022 0.002 TYR C 483 ARG 0.019 0.001 ARG D 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 239 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 GLU cc_start: 0.8240 (mp0) cc_final: 0.7957 (mp0) REVERT: B 377 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8168 (mppt) REVERT: C 80 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: C 147 MET cc_start: 0.8916 (mmp) cc_final: 0.8644 (mmp) REVERT: C 395 PHE cc_start: 0.7512 (m-80) cc_final: 0.7071 (m-80) REVERT: C 412 PHE cc_start: 0.7885 (t80) cc_final: 0.7679 (t80) REVERT: C 577 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7196 (t0) REVERT: C 585 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6612 (tpt) REVERT: D 295 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6778 (mpt180) REVERT: D 467 ASP cc_start: 0.8082 (t0) cc_final: 0.7829 (t0) REVERT: E 188 MET cc_start: 0.8799 (mpt) cc_final: 0.8318 (mpt) REVERT: E 357 ILE cc_start: 0.7974 (mm) cc_final: 0.7612 (mm) REVERT: E 367 LYS cc_start: 0.8696 (pptt) cc_final: 0.8272 (tmmm) REVERT: E 449 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7337 (mtp85) REVERT: F 8 HIS cc_start: 0.8663 (t-170) cc_final: 0.8096 (t70) REVERT: F 67 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: F 71 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: F 80 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: F 275 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.5767 (ptmm) REVERT: F 277 TYR cc_start: 0.7888 (m-80) cc_final: 0.7499 (m-80) REVERT: F 279 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7558 (tppt) REVERT: F 351 CYS cc_start: 0.8124 (m) cc_final: 0.7860 (m) REVERT: F 354 MET cc_start: 0.6135 (mmp) cc_final: 0.5643 (mmp) REVERT: F 417 GLN cc_start: 0.8798 (tt0) cc_final: 0.8003 (mm-40) REVERT: F 424 ARG cc_start: 0.7497 (mmp80) cc_final: 0.7231 (tpp-160) REVERT: I 200 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8208 (ptmt) REVERT: I 206 GLN cc_start: 0.8981 (tt0) cc_final: 0.8432 (pt0) REVERT: I 247 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8581 (mt) REVERT: I 502 MET cc_start: 0.8947 (mmt) cc_final: 0.8657 (mmt) outliers start: 57 outliers final: 36 residues processed: 280 average time/residue: 1.4043 time to fit residues: 453.7829 Evaluate side-chains 281 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 234 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 0.0370 chunk 268 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 281 optimal weight: 0.0040 chunk 259 optimal weight: 3.9990 chunk 224 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN D 240 HIS ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 73 HIS I 327 ASN I 428 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25181 Z= 0.145 Angle : 0.555 14.638 34374 Z= 0.290 Chirality : 0.040 0.309 3914 Planarity : 0.003 0.081 4013 Dihedral : 17.461 88.435 4071 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.13 % Allowed : 17.76 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2721 helix: 1.66 (0.14), residues: 1548 sheet: 0.09 (0.32), residues: 248 loop : -0.17 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 154 HIS 0.005 0.001 HIS C 69 PHE 0.012 0.001 PHE A 880 TYR 0.014 0.001 TYR C 483 ARG 0.019 0.000 ARG D 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 259 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8578 (mptp) REVERT: A 606 GLU cc_start: 0.8212 (mp0) cc_final: 0.7929 (mp0) REVERT: B 377 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8171 (mppt) REVERT: C 80 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: C 391 PHE cc_start: 0.7722 (t80) cc_final: 0.7284 (t80) REVERT: C 395 PHE cc_start: 0.7461 (m-80) cc_final: 0.7170 (m-80) REVERT: C 412 PHE cc_start: 0.7965 (t80) cc_final: 0.7700 (t80) REVERT: C 577 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7210 (t0) REVERT: D 295 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6740 (mpt180) REVERT: D 467 ASP cc_start: 0.8051 (t0) cc_final: 0.7803 (t0) REVERT: E 357 ILE cc_start: 0.7960 (mm) cc_final: 0.7630 (mm) REVERT: E 367 LYS cc_start: 0.8681 (pptt) cc_final: 0.8249 (tmmm) REVERT: F 5 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8279 (tp40) REVERT: F 67 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: F 71 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: F 277 TYR cc_start: 0.7933 (m-80) cc_final: 0.7552 (m-80) REVERT: F 279 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7518 (tppt) REVERT: F 318 GLN cc_start: 0.6470 (mt0) cc_final: 0.5925 (mt0) REVERT: F 321 CYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7467 (p) REVERT: F 354 MET cc_start: 0.6023 (mmp) cc_final: 0.5554 (tpt) REVERT: F 417 GLN cc_start: 0.8773 (tt0) cc_final: 0.7970 (mm-40) REVERT: F 424 ARG cc_start: 0.7496 (mmp80) cc_final: 0.7225 (tpp-160) REVERT: I 200 LYS cc_start: 0.8440 (ptpp) cc_final: 0.8196 (ptmt) REVERT: I 206 GLN cc_start: 0.8916 (tt0) cc_final: 0.8375 (pt0) REVERT: I 502 MET cc_start: 0.8929 (mmt) cc_final: 0.8541 (mmt) outliers start: 29 outliers final: 17 residues processed: 280 average time/residue: 1.5353 time to fit residues: 493.0914 Evaluate side-chains 269 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 28 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 overall best weight: 3.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 600 ASN D 240 HIS F 67 GLN F 73 HIS I 428 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.108410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.073842 restraints weight = 43900.706| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.20 r_work: 0.2870 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25181 Z= 0.320 Angle : 0.613 14.553 34374 Z= 0.318 Chirality : 0.043 0.274 3914 Planarity : 0.004 0.082 4013 Dihedral : 17.618 86.715 4071 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.25 % Allowed : 17.88 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2721 helix: 1.53 (0.14), residues: 1558 sheet: 0.20 (0.32), residues: 245 loop : -0.22 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 154 HIS 0.004 0.001 HIS D 323 PHE 0.019 0.001 PHE C 455 TYR 0.021 0.001 TYR C 483 ARG 0.019 0.001 ARG D 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9045.46 seconds wall clock time: 159 minutes 54.15 seconds (9594.15 seconds total)