Starting phenix.real_space_refine on Mon Oct 14 16:31:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/10_2024/8h69_34497.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/10_2024/8h69_34497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/10_2024/8h69_34497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/10_2024/8h69_34497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/10_2024/8h69_34497.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h69_34497/10_2024/8h69_34497.cif" } resolution = 3.7 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 128 5.16 5 C 11214 2.51 5 N 3150 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18028 Number of models: 1 Model: "" Number of chains: 5 Chain: "3" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 12} Chain: "5" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "A" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5790 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 33, 'TRANS': 682} Chain: "B" Number of atoms: 6022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6022 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 32, 'TRANS': 721} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5436 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 27, 'TRANS': 655} Time building chain proxies: 9.99, per 1000 atoms: 0.55 Number of scatterers: 18028 At special positions: 0 Unit cell: (136.24, 123.76, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 36 15.00 O 3500 8.00 N 3150 7.00 C 11214 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: 4.56 Conformation dependent library (CDL) restraints added in 2.3 seconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 22 sheets defined 42.3% alpha, 11.5% beta 8 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.653A pdb=" N LEU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 48 removed outlier: 3.817A pdb=" N CYS A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.600A pdb=" N TRP A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.998A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.014A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.864A pdb=" N GLY A 186 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.059A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.570A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.643A pdb=" N ILE A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 removed outlier: 4.083A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.762A pdb=" N TRP A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.629A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.553A pdb=" N TYR A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.549A pdb=" N GLU A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 598 removed outlier: 4.040A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 596 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.730A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.722A pdb=" N PHE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.774A pdb=" N ARG A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 641 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 removed outlier: 3.882A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 674 removed outlier: 4.347A pdb=" N ILE A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.624A pdb=" N SER A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.882A pdb=" N PHE B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.516A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.568A pdb=" N THR B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.209A pdb=" N GLU B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.506A pdb=" N SER B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.678A pdb=" N ASN B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.718A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.705A pdb=" N VAL B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.671A pdb=" N ARG B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 266 removed outlier: 4.075A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 removed outlier: 3.666A pdb=" N LYS B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.503A pdb=" N THR B 291 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.650A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.760A pdb=" N LYS B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.780A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.613A pdb=" N ASP B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 525 through 534 removed outlier: 3.546A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.647A pdb=" N LYS B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.766A pdb=" N LYS B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.919A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.658A pdb=" N ASP B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 removed outlier: 4.307A pdb=" N GLN B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.502A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.652A pdb=" N ILE B 682 " --> pdb=" O GLN B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 701 through 705 removed outlier: 4.059A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 removed outlier: 3.848A pdb=" N VAL B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 728 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 removed outlier: 3.541A pdb=" N GLU B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 747 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 748 " --> pdb=" O MET B 744 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 removed outlier: 4.407A pdb=" N GLU C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.594A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.179A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.525A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.635A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.756A pdb=" N PHE C 168 " --> pdb=" O MET C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.673A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.870A pdb=" N ILE C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.569A pdb=" N LEU C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 273 removed outlier: 4.049A pdb=" N ILE C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.691A pdb=" N LEU C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.894A pdb=" N MET C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.662A pdb=" N ARG C 436 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 541 through 556 removed outlier: 3.551A pdb=" N LEU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 554 " --> pdb=" O TYR C 550 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 555 " --> pdb=" O GLN C 551 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 566 removed outlier: 3.877A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.593A pdb=" N SER C 582 " --> pdb=" O SER C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.598A pdb=" N THR C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 removed outlier: 3.762A pdb=" N ILE C 616 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 619 " --> pdb=" O ILE C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.883A pdb=" N ALA C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 624' Processing helix chain 'C' and resid 677 through 682 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.209A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.007A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.560A pdb=" N VAL A 557 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 559 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.588A pdb=" N ARG B 365 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 355 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.691A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.637A pdb=" N GLN B 210 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.619A pdb=" N THR B 204 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 202 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.930A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.621A pdb=" N PHE B 490 " --> pdb=" O TYR B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 643 through 644 removed outlier: 3.683A pdb=" N ALA B 643 " --> pdb=" O MET B 655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.339A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 134 removed outlier: 4.448A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 147 removed outlier: 3.679A pdb=" N ILE C 141 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.593A pdb=" N ILE C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.965A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER C 481 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 386 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 478 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE C 463 " --> pdb=" O VAL C 478 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 470 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 636 through 639 removed outlier: 3.530A pdb=" N LEU C 636 " --> pdb=" O ILE C 647 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.565A pdb=" N ASN C 659 " --> pdb=" O ARG C 664 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 664 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4003 1.33 - 1.45: 4105 1.45 - 1.57: 10050 1.57 - 1.69: 71 1.69 - 1.81: 224 Bond restraints: 18453 Sorted by residual: bond pdb=" CA PHE A 205 " pdb=" CB PHE A 205 " ideal model delta sigma weight residual 1.525 1.472 0.053 1.47e-02 4.63e+03 1.29e+01 bond pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.41e-02 5.03e+03 1.26e+01 bond pdb=" N ASN C 429 " pdb=" CA ASN C 429 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" N ARG C 427 " pdb=" CA ARG C 427 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.45e+00 bond pdb=" N ARG C 423 " pdb=" CA ARG C 423 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 ... (remaining 18448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 23518 2.11 - 4.23: 1297 4.23 - 6.34: 183 6.34 - 8.46: 46 8.46 - 10.57: 14 Bond angle restraints: 25058 Sorted by residual: angle pdb=" N VAL B 286 " pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 113.16 103.05 10.11 1.49e+00 4.50e-01 4.60e+01 angle pdb=" N ALA C 587 " pdb=" CA ALA C 587 " pdb=" C ALA C 587 " ideal model delta sigma weight residual 112.23 104.58 7.65 1.26e+00 6.30e-01 3.69e+01 angle pdb=" C HIS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" N LEU B 271 " pdb=" CA LEU B 271 " pdb=" C LEU B 271 " ideal model delta sigma weight residual 113.16 120.52 -7.36 1.42e+00 4.96e-01 2.68e+01 angle pdb=" N VAL C 421 " pdb=" CA VAL C 421 " pdb=" C VAL C 421 " ideal model delta sigma weight residual 109.34 98.77 10.57 2.08e+00 2.31e-01 2.58e+01 ... (remaining 25053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 10548 17.69 - 35.37: 609 35.37 - 53.06: 134 53.06 - 70.75: 53 70.75 - 88.43: 13 Dihedral angle restraints: 11357 sinusoidal: 5090 harmonic: 6267 Sorted by residual: dihedral pdb=" CA CYS C 239 " pdb=" C CYS C 239 " pdb=" N TRP C 240 " pdb=" CA TRP C 240 " ideal model delta harmonic sigma weight residual -180.00 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLN B 545 " pdb=" C GLN B 545 " pdb=" N MET B 546 " pdb=" CA MET B 546 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LYS C 197 " pdb=" C LYS C 197 " pdb=" N ILE C 198 " pdb=" CA ILE C 198 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 11354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1906 0.057 - 0.113: 698 0.113 - 0.170: 154 0.170 - 0.226: 24 0.226 - 0.283: 8 Chirality restraints: 2790 Sorted by residual: chirality pdb=" CA LEU B 224 " pdb=" N LEU B 224 " pdb=" C LEU B 224 " pdb=" CB LEU B 224 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 450 " pdb=" CA ILE B 450 " pdb=" CG1 ILE B 450 " pdb=" CG2 ILE B 450 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CG LEU B 604 " pdb=" CB LEU B 604 " pdb=" CD1 LEU B 604 " pdb=" CD2 LEU B 604 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2787 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 633 " 0.035 2.00e-02 2.50e+03 2.86e-02 1.44e+01 pdb=" CG PHE C 633 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 633 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 633 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 633 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE C 633 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 633 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 537 " 0.013 2.00e-02 2.50e+03 1.88e-02 8.87e+00 pdb=" CG TRP A 537 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 537 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 537 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 537 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 537 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 537 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 537 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 344 " 0.020 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE B 344 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 344 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 344 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 344 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 344 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 344 " 0.010 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 126 2.51 - 3.11: 12856 3.11 - 3.71: 28482 3.71 - 4.30: 41001 4.30 - 4.90: 64994 Nonbonded interactions: 147459 Sorted by model distance: nonbonded pdb=" O ASN C 425 " pdb=" O GLN C 426 " model vdw 1.917 3.040 nonbonded pdb=" OG SER C 273 " pdb=" OE1 GLU C 578 " model vdw 2.196 3.040 nonbonded pdb=" N GLN C 426 " pdb=" OE1 GLN C 426 " model vdw 2.197 3.120 nonbonded pdb=" O SER B 293 " pdb=" OG SER C 643 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR C 129 " pdb=" OG1 THR C 245 " model vdw 2.259 3.040 ... (remaining 147454 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 44.460 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.009 0.082 18453 Z= 0.585 Angle : 1.121 10.572 25058 Z= 0.630 Chirality : 0.061 0.283 2790 Planarity : 0.007 0.060 3100 Dihedral : 12.846 88.432 7299 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 1.52 % Allowed : 3.98 % Favored : 94.50 % 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: -4.98 (0.14), residues: 2147 helix: -4.07 (0.09), residues: 819 sheet: -2.19 (0.33), residues: 214 loop : -2.92 (0.16), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP A 537 HIS 0.008 0.002 HIS A 326 PHE 0.060 0.004 PHE C 633 TYR 0.044 0.004 TYR B 30 ARG 0.017 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 533 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4501 (ptp) cc_final: 0.4051 (mtm) REVERT: A 79 ILE cc_start: 0.8001 (mt) cc_final: 0.7784 (mp) REVERT: A 86 MET cc_start: 0.8795 (tpt) cc_final: 0.8517 (tpt) REVERT: A 342 LEU cc_start: 0.8745 (tp) cc_final: 0.8477 (tp) REVERT: A 540 TYR cc_start: 0.9020 (m-80) cc_final: 0.8700 (m-10) REVERT: A 674 ASP cc_start: 0.6162 (t0) cc_final: 0.5854 (t0) REVERT: B 49 TYR cc_start: 0.8897 (m-80) cc_final: 0.8662 (m-10) REVERT: B 87 CYS cc_start: 0.7974 (m) cc_final: 0.7773 (m) REVERT: B 281 LYS cc_start: 0.8027 (mttt) cc_final: 0.7423 (mtpp) REVERT: B 303 THR cc_start: 0.9213 (m) cc_final: 0.8978 (p) REVERT: B 322 ILE cc_start: 0.9280 (pp) cc_final: 0.9065 (pt) REVERT: B 518 ASN cc_start: 0.7223 (m110) cc_final: 0.7007 (m-40) REVERT: B 537 ASN cc_start: 0.8220 (m-40) cc_final: 0.7339 (t0) REVERT: B 663 THR cc_start: 0.8209 (p) cc_final: 0.7995 (m) REVERT: B 665 SER cc_start: 0.8471 (m) cc_final: 0.8150 (t) REVERT: B 720 SER cc_start: 0.8976 (m) cc_final: 0.8543 (t) REVERT: C 46 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.6895 (mmt180) REVERT: C 47 MET cc_start: 0.7108 (tpp) cc_final: 0.6699 (tpp) REVERT: C 160 GLN cc_start: 0.8137 (mt0) cc_final: 0.7708 (pt0) REVERT: C 217 PHE cc_start: 0.6133 (p90) cc_final: 0.5735 (p90) REVERT: C 285 HIS cc_start: 0.6643 (m-70) cc_final: 0.6064 (m-70) REVERT: C 402 MET cc_start: -0.0513 (mtt) cc_final: -0.1115 (mtp) REVERT: C 428 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3960 (mp) REVERT: C 526 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7409 (tptt) REVERT: C 535 MET cc_start: 0.6616 (mpm) cc_final: 0.5787 (mmm) REVERT: C 536 MET cc_start: 0.3010 (pmm) cc_final: 0.2239 (pmm) REVERT: C 543 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5742 (mm-30) REVERT: C 589 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.3984 (mtp180) outliers start: 29 outliers final: 4 residues processed: 550 average time/residue: 0.3776 time to fit residues: 296.8482 Evaluate side-chains 339 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 331 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 526 LYS Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 0.0270 chunk 55 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 196 optimal weight: 50.0000 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 350 ASN A 519 ASN A 670 GLN B 58 ASN B 153 ASN B 284 ASN B 292 ASN B 306 ASN B 310 ASN B 329 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS C 110 HIS C 134 HIS C 182 GLN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18453 Z= 0.202 Angle : 0.701 10.986 25058 Z= 0.367 Chirality : 0.045 0.308 2790 Planarity : 0.005 0.056 3100 Dihedral : 12.345 84.287 2927 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.78 % Allowed : 11.84 % Favored : 85.39 % 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: -3.79 (0.15), residues: 2147 helix: -2.61 (0.14), residues: 852 sheet: -2.18 (0.32), residues: 232 loop : -2.46 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 537 HIS 0.011 0.001 HIS C 110 PHE 0.040 0.002 PHE C 595 TYR 0.018 0.002 TYR C 205 ARG 0.008 0.001 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 409 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4699 (ptp) cc_final: 0.4284 (mtm) REVERT: A 524 GLU cc_start: 0.7819 (mp0) cc_final: 0.7375 (mp0) REVERT: A 540 TYR cc_start: 0.9005 (m-80) cc_final: 0.8802 (m-80) REVERT: A 564 TYR cc_start: 0.8752 (m-80) cc_final: 0.8156 (m-80) REVERT: A 674 ASP cc_start: 0.6309 (t0) cc_final: 0.5860 (t0) REVERT: B 41 ASP cc_start: 0.7839 (t0) cc_final: 0.7581 (t0) REVERT: B 87 CYS cc_start: 0.7884 (m) cc_final: 0.7548 (m) REVERT: B 126 ARG cc_start: 0.7387 (mtm110) cc_final: 0.7011 (ptm160) REVERT: B 277 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7325 (mt-10) REVERT: B 284 ASN cc_start: 0.7934 (m-40) cc_final: 0.7650 (m110) REVERT: B 303 THR cc_start: 0.9107 (m) cc_final: 0.8901 (p) REVERT: B 478 SER cc_start: 0.8772 (t) cc_final: 0.8287 (p) REVERT: B 537 ASN cc_start: 0.8288 (m-40) cc_final: 0.8076 (t0) REVERT: B 601 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8637 (tt) REVERT: B 604 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8300 (mp) REVERT: B 665 SER cc_start: 0.8579 (m) cc_final: 0.8191 (t) REVERT: C 28 MET cc_start: 0.7397 (tmm) cc_final: 0.7155 (tmm) REVERT: C 32 LYS cc_start: 0.7874 (tptp) cc_final: 0.7629 (tppt) REVERT: C 47 MET cc_start: 0.7229 (tpp) cc_final: 0.6710 (tpp) REVERT: C 51 MET cc_start: 0.8045 (mmm) cc_final: 0.7625 (mmm) REVERT: C 136 ARG cc_start: 0.5417 (ppt170) cc_final: 0.5025 (mmt90) REVERT: C 160 GLN cc_start: 0.7938 (mt0) cc_final: 0.7634 (tt0) REVERT: C 171 GLU cc_start: 0.7892 (mp0) cc_final: 0.7678 (pm20) REVERT: C 230 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7253 (mm-30) REVERT: C 402 MET cc_start: -0.0318 (mtt) cc_final: -0.0738 (mtp) REVERT: C 405 SER cc_start: 0.4226 (p) cc_final: 0.3734 (t) REVERT: C 428 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.3976 (mt) outliers start: 53 outliers final: 22 residues processed: 436 average time/residue: 0.3470 time to fit residues: 223.0855 Evaluate side-chains 346 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 321 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN B 676 ASN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18453 Z= 0.272 Angle : 0.700 10.445 25058 Z= 0.363 Chirality : 0.045 0.224 2790 Planarity : 0.005 0.048 3100 Dihedral : 12.023 81.888 2912 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.78 % Allowed : 13.93 % Favored : 83.29 % 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: -3.10 (0.16), residues: 2147 helix: -1.85 (0.16), residues: 851 sheet: -2.24 (0.31), residues: 230 loop : -2.14 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 537 HIS 0.003 0.001 HIS A 510 PHE 0.039 0.002 PHE C 595 TYR 0.025 0.002 TYR B 689 ARG 0.005 0.001 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 338 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4654 (ptp) cc_final: 0.4041 (mtm) REVERT: A 84 ARG cc_start: 0.7789 (mmm160) cc_final: 0.7581 (mmm160) REVERT: A 155 MET cc_start: -0.0033 (OUTLIER) cc_final: -0.0251 (ptp) REVERT: A 234 ASP cc_start: 0.7583 (p0) cc_final: 0.7380 (p0) REVERT: A 257 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 524 GLU cc_start: 0.8191 (mp0) cc_final: 0.7709 (mp0) REVERT: A 537 TRP cc_start: 0.8066 (m-90) cc_final: 0.7295 (m-10) REVERT: A 548 MET cc_start: 0.7272 (pmm) cc_final: 0.6975 (pmm) REVERT: A 564 TYR cc_start: 0.8935 (m-80) cc_final: 0.8073 (m-80) REVERT: A 595 MET cc_start: 0.8035 (mtp) cc_final: 0.7763 (mtm) REVERT: A 609 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7145 (tptt) REVERT: B 126 ARG cc_start: 0.7520 (mtm110) cc_final: 0.7178 (ptm160) REVERT: B 176 LYS cc_start: 0.8112 (mppt) cc_final: 0.7839 (mtmt) REVERT: B 179 MET cc_start: 0.7406 (mmm) cc_final: 0.7029 (mmm) REVERT: B 284 ASN cc_start: 0.7961 (m-40) cc_final: 0.7722 (m110) REVERT: B 303 THR cc_start: 0.9213 (m) cc_final: 0.8946 (p) REVERT: B 497 TYR cc_start: 0.8288 (t80) cc_final: 0.8015 (t80) REVERT: B 537 ASN cc_start: 0.8620 (m-40) cc_final: 0.8131 (t0) REVERT: B 601 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8740 (tt) REVERT: B 665 SER cc_start: 0.8648 (m) cc_final: 0.8317 (t) REVERT: B 705 TYR cc_start: 0.8447 (t80) cc_final: 0.8241 (t80) REVERT: C 28 MET cc_start: 0.7460 (tmm) cc_final: 0.7209 (tmm) REVERT: C 47 MET cc_start: 0.7251 (tpp) cc_final: 0.6703 (tpp) REVERT: C 51 MET cc_start: 0.8140 (mmm) cc_final: 0.7744 (mmm) REVERT: C 160 GLN cc_start: 0.7906 (mt0) cc_final: 0.7399 (tt0) REVERT: C 163 ILE cc_start: 0.8784 (mm) cc_final: 0.8510 (mm) REVERT: C 164 MET cc_start: 0.7954 (mmt) cc_final: 0.7665 (mmp) REVERT: C 171 GLU cc_start: 0.7999 (mp0) cc_final: 0.7560 (pm20) REVERT: C 187 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8554 (pptt) REVERT: C 217 PHE cc_start: 0.5429 (p90) cc_final: 0.5079 (p90) REVERT: C 229 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8531 (tt) REVERT: C 230 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7428 (mm-30) REVERT: C 294 MET cc_start: 0.6740 (ppp) cc_final: 0.6405 (ppp) REVERT: C 407 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.4353 (mp0) REVERT: C 428 LEU cc_start: 0.4459 (OUTLIER) cc_final: 0.4047 (mt) REVERT: C 467 MET cc_start: 0.3336 (mpp) cc_final: 0.3097 (mpp) outliers start: 53 outliers final: 29 residues processed: 368 average time/residue: 0.3448 time to fit residues: 186.1087 Evaluate side-chains 340 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.0670 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 208 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18453 Z= 0.180 Angle : 0.642 11.046 25058 Z= 0.329 Chirality : 0.043 0.280 2790 Planarity : 0.004 0.103 3100 Dihedral : 11.795 80.454 2911 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.09 % Allowed : 15.45 % Favored : 81.46 % 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: -2.64 (0.17), residues: 2147 helix: -1.37 (0.17), residues: 850 sheet: -2.07 (0.31), residues: 232 loop : -1.94 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 537 HIS 0.004 0.001 HIS A 510 PHE 0.031 0.002 PHE C 595 TYR 0.027 0.001 TYR B 689 ARG 0.006 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 349 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4579 (ptp) cc_final: 0.4012 (mtm) REVERT: A 410 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7690 (mt-10) REVERT: A 524 GLU cc_start: 0.8137 (mp0) cc_final: 0.7806 (mp0) REVERT: A 536 LYS cc_start: 0.8895 (tttt) cc_final: 0.8557 (ttmt) REVERT: A 537 TRP cc_start: 0.8098 (m-90) cc_final: 0.7242 (m-10) REVERT: A 548 MET cc_start: 0.7286 (pmm) cc_final: 0.6963 (pmm) REVERT: A 564 TYR cc_start: 0.8933 (m-80) cc_final: 0.8023 (m-80) REVERT: A 595 MET cc_start: 0.8016 (mtp) cc_final: 0.7772 (mtm) REVERT: A 609 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7119 (tptt) REVERT: A 661 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: B 126 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7146 (ptm160) REVERT: B 179 MET cc_start: 0.7336 (mmm) cc_final: 0.6972 (mmm) REVERT: B 284 ASN cc_start: 0.7915 (m-40) cc_final: 0.7580 (m110) REVERT: B 303 THR cc_start: 0.9126 (m) cc_final: 0.8798 (p) REVERT: B 379 LYS cc_start: 0.8276 (tmmt) cc_final: 0.8070 (tmmt) REVERT: B 407 MET cc_start: 0.7058 (mmt) cc_final: 0.6736 (mmm) REVERT: B 497 TYR cc_start: 0.8192 (t80) cc_final: 0.7918 (t80) REVERT: B 537 ASN cc_start: 0.8562 (m-40) cc_final: 0.7996 (t0) REVERT: B 665 SER cc_start: 0.8552 (m) cc_final: 0.8346 (t) REVERT: B 679 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7078 (tp-100) REVERT: C 47 MET cc_start: 0.7168 (tpp) cc_final: 0.6561 (tpp) REVERT: C 51 MET cc_start: 0.8091 (mmm) cc_final: 0.7778 (mmm) REVERT: C 160 GLN cc_start: 0.7914 (mt0) cc_final: 0.7551 (tt0) REVERT: C 164 MET cc_start: 0.7985 (mmt) cc_final: 0.7746 (mmm) REVERT: C 171 GLU cc_start: 0.7877 (mp0) cc_final: 0.7497 (pm20) REVERT: C 209 ARG cc_start: 0.7207 (tpm170) cc_final: 0.6900 (tpm170) REVERT: C 217 PHE cc_start: 0.5338 (p90) cc_final: 0.4978 (p90) REVERT: C 230 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7205 (mm-30) REVERT: C 285 HIS cc_start: 0.7683 (m-70) cc_final: 0.7265 (m90) REVERT: C 294 MET cc_start: 0.6786 (ppp) cc_final: 0.6492 (ppp) REVERT: C 428 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.4011 (mt) REVERT: C 467 MET cc_start: 0.3469 (mpp) cc_final: 0.3210 (mpp) REVERT: C 536 MET cc_start: 0.2632 (pmm) cc_final: 0.1964 (pmm) outliers start: 59 outliers final: 29 residues processed: 380 average time/residue: 0.3176 time to fit residues: 181.8611 Evaluate side-chains 337 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 305 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 155 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 499 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18453 Z= 0.174 Angle : 0.629 10.920 25058 Z= 0.321 Chirality : 0.043 0.226 2790 Planarity : 0.004 0.056 3100 Dihedral : 11.621 79.490 2911 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.99 % Allowed : 16.40 % Favored : 80.62 % 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: -2.37 (0.17), residues: 2147 helix: -1.12 (0.17), residues: 850 sheet: -1.82 (0.33), residues: 221 loop : -1.84 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 537 HIS 0.004 0.001 HIS A 510 PHE 0.032 0.001 PHE C 595 TYR 0.023 0.001 TYR B 689 ARG 0.005 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 335 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4102 (ptp) cc_final: 0.3485 (mtm) REVERT: A 207 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7292 (mt) REVERT: A 410 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: A 524 GLU cc_start: 0.8168 (mp0) cc_final: 0.7952 (mp0) REVERT: A 536 LYS cc_start: 0.8913 (tttt) cc_final: 0.8583 (ttmt) REVERT: A 537 TRP cc_start: 0.8089 (m-90) cc_final: 0.7202 (m-10) REVERT: A 564 TYR cc_start: 0.8874 (m-80) cc_final: 0.7880 (m-80) REVERT: A 609 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7223 (tptt) REVERT: A 661 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: A 670 GLN cc_start: 0.7274 (tp40) cc_final: 0.7014 (tp40) REVERT: A 674 ASP cc_start: 0.7972 (m-30) cc_final: 0.7741 (m-30) REVERT: B 126 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7300 (ptm160) REVERT: B 179 MET cc_start: 0.7481 (mmm) cc_final: 0.7167 (mmm) REVERT: B 277 GLU cc_start: 0.8018 (tm-30) cc_final: 0.6951 (tp30) REVERT: B 284 ASN cc_start: 0.7832 (m-40) cc_final: 0.7472 (m110) REVERT: B 303 THR cc_start: 0.9113 (m) cc_final: 0.8778 (p) REVERT: B 358 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7118 (tm-30) REVERT: B 379 LYS cc_start: 0.8293 (tmmt) cc_final: 0.8002 (tmmt) REVERT: B 497 TYR cc_start: 0.8258 (t80) cc_final: 0.7958 (t80) REVERT: B 537 ASN cc_start: 0.8474 (m-40) cc_final: 0.7869 (t0) REVERT: B 665 SER cc_start: 0.8568 (m) cc_final: 0.8349 (t) REVERT: B 705 TYR cc_start: 0.8275 (t80) cc_final: 0.7673 (t80) REVERT: C 47 MET cc_start: 0.7353 (tpp) cc_final: 0.6914 (tpp) REVERT: C 51 MET cc_start: 0.8095 (mmm) cc_final: 0.7826 (mmm) REVERT: C 171 GLU cc_start: 0.7833 (mp0) cc_final: 0.7466 (pm20) REVERT: C 187 LYS cc_start: 0.8288 (pptt) cc_final: 0.7640 (mtmt) REVERT: C 229 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8516 (tt) REVERT: C 294 MET cc_start: 0.6900 (ppp) cc_final: 0.6624 (ppp) REVERT: C 428 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4099 (mt) REVERT: C 467 MET cc_start: 0.3594 (mpp) cc_final: 0.3373 (mpp) REVERT: C 536 MET cc_start: 0.2392 (pmm) cc_final: 0.1873 (pmm) outliers start: 57 outliers final: 30 residues processed: 364 average time/residue: 0.3256 time to fit residues: 177.0122 Evaluate side-chains 340 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.6980 chunk 188 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 173 optimal weight: 0.2980 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18453 Z= 0.219 Angle : 0.659 10.139 25058 Z= 0.336 Chirality : 0.044 0.276 2790 Planarity : 0.004 0.050 3100 Dihedral : 11.608 79.172 2911 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.46 % Allowed : 17.02 % Favored : 79.52 % 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: -2.23 (0.17), residues: 2147 helix: -1.02 (0.17), residues: 850 sheet: -1.83 (0.33), residues: 236 loop : -1.72 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 537 HIS 0.004 0.001 HIS A 437 PHE 0.041 0.002 PHE B 740 TYR 0.023 0.001 TYR A 130 ARG 0.007 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 323 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4258 (ptp) cc_final: 0.3628 (mtm) REVERT: A 257 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 335 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8578 (tt) REVERT: A 410 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 536 LYS cc_start: 0.8998 (tttt) cc_final: 0.8587 (ttmt) REVERT: A 537 TRP cc_start: 0.8195 (m-90) cc_final: 0.7258 (m-10) REVERT: A 564 TYR cc_start: 0.8895 (m-80) cc_final: 0.8510 (m-80) REVERT: A 609 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7347 (tptt) REVERT: A 661 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: A 670 GLN cc_start: 0.7180 (tp40) cc_final: 0.6732 (tp40) REVERT: B 126 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7346 (ptm160) REVERT: B 179 MET cc_start: 0.7540 (mmm) cc_final: 0.7272 (mmm) REVERT: B 277 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7335 (mt-10) REVERT: B 284 ASN cc_start: 0.7787 (m-40) cc_final: 0.7521 (m110) REVERT: B 303 THR cc_start: 0.9167 (m) cc_final: 0.8834 (p) REVERT: B 358 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 497 TYR cc_start: 0.8254 (t80) cc_final: 0.8003 (t80) REVERT: B 537 ASN cc_start: 0.8536 (m-40) cc_final: 0.7887 (t0) REVERT: B 656 GLU cc_start: 0.7812 (pm20) cc_final: 0.7592 (pm20) REVERT: B 665 SER cc_start: 0.8616 (m) cc_final: 0.8339 (t) REVERT: C 39 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7121 (tp40) REVERT: C 47 MET cc_start: 0.7316 (tpp) cc_final: 0.6853 (tpp) REVERT: C 51 MET cc_start: 0.8098 (mmm) cc_final: 0.7867 (mmm) REVERT: C 89 VAL cc_start: 0.8267 (m) cc_final: 0.8018 (p) REVERT: C 209 ARG cc_start: 0.7129 (tpm170) cc_final: 0.6702 (tpm170) REVERT: C 294 MET cc_start: 0.6900 (ppp) cc_final: 0.6628 (ppp) REVERT: C 428 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4188 (mt) REVERT: C 467 MET cc_start: 0.3922 (mpp) cc_final: 0.3535 (mpp) REVERT: C 536 MET cc_start: 0.2531 (pmm) cc_final: 0.2152 (pmm) REVERT: C 542 PRO cc_start: 0.6232 (Cg_exo) cc_final: 0.5875 (Cg_endo) REVERT: C 543 GLU cc_start: 0.3419 (mp0) cc_final: 0.3161 (mp0) outliers start: 66 outliers final: 38 residues processed: 359 average time/residue: 0.3275 time to fit residues: 176.5984 Evaluate side-chains 340 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 295 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 551 GLN Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 116 optimal weight: 0.0670 chunk 208 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 126 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS B 16 ASN B 136 ASN B 153 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18453 Z= 0.161 Angle : 0.637 10.219 25058 Z= 0.321 Chirality : 0.043 0.285 2790 Planarity : 0.004 0.055 3100 Dihedral : 11.464 79.409 2911 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.72 % Allowed : 17.71 % Favored : 79.57 % 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: -2.08 (0.17), residues: 2147 helix: -0.86 (0.18), residues: 841 sheet: -1.73 (0.33), residues: 238 loop : -1.68 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 537 HIS 0.005 0.001 HIS A 437 PHE 0.038 0.001 PHE B 740 TYR 0.022 0.001 TYR C 205 ARG 0.010 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 329 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4222 (ptp) cc_final: 0.3627 (mtm) REVERT: A 410 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: A 536 LYS cc_start: 0.8953 (tttt) cc_final: 0.8406 (ttmt) REVERT: A 537 TRP cc_start: 0.8125 (m-90) cc_final: 0.7113 (m-10) REVERT: A 548 MET cc_start: 0.7113 (pmm) cc_final: 0.6577 (pmm) REVERT: A 564 TYR cc_start: 0.8909 (m-80) cc_final: 0.8480 (m-80) REVERT: A 566 ARG cc_start: 0.8016 (tmt170) cc_final: 0.7610 (ttt-90) REVERT: A 609 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7291 (tptt) REVERT: A 661 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: A 670 GLN cc_start: 0.7087 (tp40) cc_final: 0.6624 (tp40) REVERT: B 45 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7248 (mtm180) REVERT: B 179 MET cc_start: 0.7517 (mmm) cc_final: 0.7195 (mmm) REVERT: B 284 ASN cc_start: 0.7815 (m-40) cc_final: 0.7593 (m110) REVERT: B 303 THR cc_start: 0.9095 (m) cc_final: 0.8723 (p) REVERT: B 358 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 407 MET cc_start: 0.6868 (mmt) cc_final: 0.6472 (mmm) REVERT: B 537 ASN cc_start: 0.8470 (m-40) cc_final: 0.7952 (t0) REVERT: B 665 SER cc_start: 0.8622 (m) cc_final: 0.8279 (t) REVERT: C 47 MET cc_start: 0.7219 (tpp) cc_final: 0.6650 (tpp) REVERT: C 48 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7856 (mttt) REVERT: C 89 VAL cc_start: 0.8243 (m) cc_final: 0.8020 (p) REVERT: C 187 LYS cc_start: 0.8340 (pptt) cc_final: 0.7792 (mtmt) REVERT: C 229 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8516 (tt) REVERT: C 244 TYR cc_start: 0.8567 (t80) cc_final: 0.8366 (t80) REVERT: C 283 MET cc_start: 0.4916 (mtp) cc_final: 0.4614 (mtp) REVERT: C 294 MET cc_start: 0.6834 (ppp) cc_final: 0.6565 (ppp) REVERT: C 305 GLU cc_start: 0.7005 (tm-30) cc_final: 0.4860 (mp0) REVERT: C 428 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.4121 (mt) REVERT: C 542 PRO cc_start: 0.6203 (Cg_exo) cc_final: 0.5900 (Cg_endo) REVERT: C 543 GLU cc_start: 0.3345 (mp0) cc_final: 0.3117 (mp0) REVERT: C 604 ARG cc_start: 0.4326 (mpt-90) cc_final: 0.3951 (mmp80) outliers start: 52 outliers final: 26 residues processed: 355 average time/residue: 0.3391 time to fit residues: 180.9895 Evaluate side-chains 334 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 303 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 551 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 102 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 136 ASN B 276 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18453 Z= 0.204 Angle : 0.668 10.104 25058 Z= 0.337 Chirality : 0.044 0.259 2790 Planarity : 0.004 0.055 3100 Dihedral : 11.471 79.049 2911 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.72 % Allowed : 18.60 % Favored : 78.68 % 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: -2.04 (0.17), residues: 2147 helix: -0.81 (0.17), residues: 848 sheet: -1.70 (0.34), residues: 239 loop : -1.68 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 706 HIS 0.006 0.001 HIS A 437 PHE 0.032 0.002 PHE C 595 TYR 0.031 0.001 TYR C 205 ARG 0.010 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 301 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4258 (ptp) cc_final: 0.3645 (mtm) REVERT: A 257 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8829 (mp) REVERT: A 410 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: A 536 LYS cc_start: 0.8866 (tttt) cc_final: 0.8633 (ttmt) REVERT: A 537 TRP cc_start: 0.8193 (m-90) cc_final: 0.7232 (m-10) REVERT: A 564 TYR cc_start: 0.8953 (m-80) cc_final: 0.8593 (m-80) REVERT: A 566 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7506 (ttt-90) REVERT: A 609 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7381 (tptt) REVERT: A 661 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: A 670 GLN cc_start: 0.7234 (tp40) cc_final: 0.6689 (tp40) REVERT: B 133 LEU cc_start: 0.8913 (mm) cc_final: 0.8588 (mp) REVERT: B 179 MET cc_start: 0.7482 (mmm) cc_final: 0.7183 (mmm) REVERT: B 284 ASN cc_start: 0.7901 (m-40) cc_final: 0.7578 (m110) REVERT: B 303 THR cc_start: 0.9122 (m) cc_final: 0.8772 (p) REVERT: B 358 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 407 MET cc_start: 0.7039 (mmt) cc_final: 0.6538 (mmm) REVERT: B 414 MET cc_start: 0.6720 (tpt) cc_final: 0.5877 (tpt) REVERT: B 537 ASN cc_start: 0.8512 (m-40) cc_final: 0.7963 (t0) REVERT: B 665 SER cc_start: 0.8615 (m) cc_final: 0.8349 (t) REVERT: C 89 VAL cc_start: 0.8256 (m) cc_final: 0.8023 (p) REVERT: C 230 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7120 (mm-30) REVERT: C 294 MET cc_start: 0.6866 (ppp) cc_final: 0.6600 (ppp) REVERT: C 428 LEU cc_start: 0.4472 (OUTLIER) cc_final: 0.4090 (mt) REVERT: C 536 MET cc_start: 0.2773 (pmm) cc_final: 0.1985 (ptt) outliers start: 52 outliers final: 32 residues processed: 330 average time/residue: 0.3274 time to fit residues: 162.7500 Evaluate side-chains 322 residues out of total 1909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 7.9990 chunk 181 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 193 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: