Starting phenix.real_space_refine on Sun Jul 21 13:12:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/07_2024/8pnp_17782.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/07_2024/8pnp_17782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/07_2024/8pnp_17782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/07_2024/8pnp_17782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/07_2024/8pnp_17782.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/07_2024/8pnp_17782.cif" } resolution = 2.49 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 88 atoms to isotropic. 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 31 5.49 5 S 103 5.16 5 C 8978 2.51 5 N 2494 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14460 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5850 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain breaks: 1 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 179 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 6, 'TRANS': 16} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.00, per 1000 atoms: 0.62 Number of scatterers: 14460 At special positions: 0 Unit cell: (94.08, 102.48, 144.48, 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 103 16.00 P 31 15.00 O 2854 8.00 N 2494 7.00 C 8978 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 - 3.50 Amino acid : False - 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: 6.01 Conformation dependent library (CDL) restraints added in 2.3 seconds 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 16 sheets defined 53.4% alpha, 12.6% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.712A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.538A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.923A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.676A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.503A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.765A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.860A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 601 removed outlier: 4.129A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.002A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.547A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.690A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.537A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.538A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.532A pdb=" N GLU B 159 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.639A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.751A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.582A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.511A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.447A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.159A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 375 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.069A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.519A pdb=" N THR B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 672 through 678 removed outlier: 6.388A pdb=" N SER B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.150A pdb=" N LEU B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.818A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.535A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.696A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.958A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.142A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.102A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.522A 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 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.321A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.682A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.334A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.338A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.908A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.725A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.986A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.514A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.965A 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 135 removed outlier: 4.721A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.355A 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 145 708 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4412 1.33 - 1.46: 2337 1.46 - 1.58: 7783 1.58 - 1.70: 64 1.70 - 1.82: 177 Bond restraints: 14773 Sorted by residual: bond pdb=" N TYR G 1 " pdb=" CA TYR G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" CB GLU C 158 " pdb=" CG GLU C 158 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.29e-01 bond pdb=" CD LYS A 361 " pdb=" CE LYS A 361 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.10e-01 ... (remaining 14768 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.62: 421 105.62 - 112.73: 7827 112.73 - 119.84: 4973 119.84 - 126.95: 6613 126.95 - 134.05: 237 Bond angle restraints: 20071 Sorted by residual: angle pdb=" CB MET C 1 " pdb=" CG MET C 1 " pdb=" SD MET C 1 " ideal model delta sigma weight residual 112.70 121.49 -8.79 3.00e+00 1.11e-01 8.59e+00 angle pdb=" CG LYS A 361 " pdb=" CD LYS A 361 " pdb=" CE LYS A 361 " ideal model delta sigma weight residual 111.30 117.88 -6.58 2.30e+00 1.89e-01 8.19e+00 angle pdb=" C2' A V 4 " pdb=" C1' A V 4 " pdb=" N9 A V 4 " ideal model delta sigma weight residual 112.00 115.46 -3.46 1.50e+00 4.44e-01 5.33e+00 angle pdb=" CB MET B 744 " pdb=" CG MET B 744 " pdb=" SD MET B 744 " ideal model delta sigma weight residual 112.70 119.51 -6.81 3.00e+00 1.11e-01 5.16e+00 angle pdb=" CA GLU C 158 " pdb=" CB GLU C 158 " pdb=" CG GLU C 158 " ideal model delta sigma weight residual 114.10 118.58 -4.48 2.00e+00 2.50e-01 5.01e+00 ... (remaining 20066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7700 17.77 - 35.54: 945 35.54 - 53.32: 300 53.32 - 71.09: 113 71.09 - 88.86: 30 Dihedral angle restraints: 9088 sinusoidal: 4079 harmonic: 5009 Sorted by residual: dihedral pdb=" CA ASP C 161 " pdb=" CB ASP C 161 " pdb=" CG ASP C 161 " pdb=" OD1 ASP C 161 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA VAL A 517 " pdb=" C VAL A 517 " pdb=" N VAL A 518 " pdb=" CA VAL A 518 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU B 78 " pdb=" CG GLU B 78 " pdb=" CD GLU B 78 " pdb=" OE1 GLU B 78 " ideal model delta sinusoidal sigma weight residual 0.00 -88.86 88.86 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1744 0.041 - 0.081: 358 0.081 - 0.122: 100 0.122 - 0.163: 11 0.163 - 0.204: 1 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CB VAL B 719 " pdb=" CA VAL B 719 " pdb=" CG1 VAL B 719 " pdb=" CG2 VAL B 719 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL B 368 " pdb=" N VAL B 368 " pdb=" C VAL B 368 " pdb=" CB VAL B 368 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2211 not shown) Planarity restraints: 2479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.41e+00 pdb=" N9 A V 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 495 " 0.173 9.50e-02 1.11e+02 7.77e-02 4.27e+00 pdb=" NE ARG A 495 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 495 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 495 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 495 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 587 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLN A 587 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN A 587 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 588 " 0.010 2.00e-02 2.50e+03 ... (remaining 2476 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 154 2.60 - 3.17: 12369 3.17 - 3.75: 23475 3.75 - 4.32: 33810 4.32 - 4.90: 54368 Nonbonded interactions: 124176 Sorted by model distance: nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.019 2.440 nonbonded pdb=" OP1 A V 6 " pdb=" O HOH V 101 " model vdw 2.085 2.440 nonbonded pdb=" OE1 GLU A 524 " pdb=" O HOH A 801 " model vdw 2.097 2.440 nonbonded pdb=" OE1 GLU A 610 " pdb=" ND2 ASN A 614 " model vdw 2.137 2.520 nonbonded pdb=" O MET C 11 " pdb=" NH1 ARG C 17 " model vdw 2.160 2.520 ... (remaining 124171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14773 Z= 0.177 Angle : 0.497 8.794 20071 Z= 0.255 Chirality : 0.037 0.204 2214 Planarity : 0.004 0.078 2479 Dihedral : 18.516 88.860 5844 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 1.24 % Allowed : 22.64 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1697 helix: 1.64 (0.19), residues: 807 sheet: -0.13 (0.38), residues: 190 loop : -0.42 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 128 PHE 0.010 0.001 PHE B 551 TYR 0.016 0.001 TYR A 305 ARG 0.013 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6162 (ppt90) cc_final: 0.5523 (ppt90) REVERT: A 222 ASN cc_start: 0.8401 (p0) cc_final: 0.8171 (p0) REVERT: B 135 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7947 (ptt90) REVERT: B 653 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7958 (mmtm) REVERT: C 146 ASP cc_start: 0.7066 (p0) cc_final: 0.6617 (p0) outliers start: 19 outliers final: 15 residues processed: 203 average time/residue: 1.4966 time to fit residues: 329.7138 Evaluate side-chains 200 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 513 ASN A 556 GLN A 670 GLN B 312 ASN B 485 ASN C 82 ASN C 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14773 Z= 0.192 Angle : 0.512 7.035 20071 Z= 0.268 Chirality : 0.039 0.161 2214 Planarity : 0.004 0.044 2479 Dihedral : 10.754 73.555 2343 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.06 % Favored : 97.88 % Rotamer: Outliers : 2.81 % Allowed : 20.03 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1697 helix: 1.75 (0.19), residues: 815 sheet: 0.23 (0.39), residues: 178 loop : -0.50 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 98 HIS 0.003 0.001 HIS B 649 PHE 0.010 0.001 PHE A 611 TYR 0.015 0.001 TYR B 555 ARG 0.008 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 1.707 Fit side-chains REVERT: A 222 ASN cc_start: 0.8393 (p0) cc_final: 0.8132 (p0) REVERT: B 75 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: B 331 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: C 64 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.7806 (mmt) REVERT: C 158 GLU cc_start: 0.5884 (mp0) cc_final: 0.5678 (mp0) outliers start: 43 outliers final: 14 residues processed: 221 average time/residue: 1.4871 time to fit residues: 356.1122 Evaluate side-chains 204 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 155 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 466 ASN A 513 ASN A 556 GLN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14773 Z= 0.220 Angle : 0.509 7.915 20071 Z= 0.266 Chirality : 0.040 0.164 2214 Planarity : 0.004 0.048 2479 Dihedral : 10.561 73.671 2327 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 2.75 % Allowed : 20.68 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1697 helix: 1.74 (0.19), residues: 815 sheet: 0.27 (0.39), residues: 178 loop : -0.53 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS A 128 PHE 0.011 0.001 PHE A 611 TYR 0.019 0.001 TYR A 305 ARG 0.002 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8397 (p0) cc_final: 0.8096 (p0) REVERT: B 75 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: B 331 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: C 64 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.7774 (mmt) REVERT: C 90 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8167 (mmt) REVERT: C 158 GLU cc_start: 0.5829 (mp0) cc_final: 0.5626 (mp0) outliers start: 42 outliers final: 19 residues processed: 219 average time/residue: 1.5604 time to fit residues: 370.1332 Evaluate side-chains 205 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 156 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 388 ASN A 556 GLN B 413 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14773 Z= 0.245 Angle : 0.523 9.388 20071 Z= 0.273 Chirality : 0.040 0.167 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.600 73.609 2327 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 2.95 % Allowed : 21.14 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1697 helix: 1.66 (0.18), residues: 816 sheet: 0.19 (0.39), residues: 181 loop : -0.59 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 368 HIS 0.004 0.001 HIS B 47 PHE 0.012 0.001 PHE B 551 TYR 0.022 0.002 TYR A 305 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6576 (ppt90) cc_final: 0.5787 (ppt-90) REVERT: A 222 ASN cc_start: 0.8365 (p0) cc_final: 0.8050 (p0) REVERT: B 75 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: B 156 THR cc_start: 0.8933 (p) cc_final: 0.8621 (p) REVERT: B 331 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: B 375 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8468 (p0) REVERT: C 6 GLU cc_start: 0.7816 (tp30) cc_final: 0.7577 (mt-10) REVERT: C 64 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.7883 (mmt) REVERT: C 90 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8128 (mmt) REVERT: C 146 ASP cc_start: 0.7072 (p0) cc_final: 0.6535 (p0) outliers start: 45 outliers final: 20 residues processed: 218 average time/residue: 1.4902 time to fit residues: 351.5492 Evaluate side-chains 205 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 184 HIS B 413 ASN B 428 GLN B 485 ASN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14773 Z= 0.341 Angle : 0.572 9.519 20071 Z= 0.300 Chirality : 0.043 0.187 2214 Planarity : 0.005 0.052 2479 Dihedral : 10.735 73.454 2325 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 3.60 % Allowed : 20.94 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1697 helix: 1.44 (0.18), residues: 823 sheet: -0.05 (0.38), residues: 188 loop : -0.73 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 368 HIS 0.005 0.001 HIS B 47 PHE 0.015 0.002 PHE B 551 TYR 0.025 0.002 TYR A 305 ARG 0.005 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 178 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5976 (OUTLIER) cc_final: 0.4465 (m110) REVERT: A 222 ASN cc_start: 0.8372 (p0) cc_final: 0.8048 (p0) REVERT: B 75 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: B 331 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: B 375 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8487 (p0) REVERT: C 6 GLU cc_start: 0.7856 (tp30) cc_final: 0.7589 (mt-10) REVERT: C 90 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8136 (mmt) REVERT: C 146 ASP cc_start: 0.7043 (p0) cc_final: 0.6538 (p0) outliers start: 55 outliers final: 28 residues processed: 213 average time/residue: 1.6250 time to fit residues: 374.3154 Evaluate side-chains 209 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 165 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 76 optimal weight: 0.0010 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 184 HIS B 413 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14773 Z= 0.154 Angle : 0.498 9.813 20071 Z= 0.258 Chirality : 0.038 0.176 2214 Planarity : 0.004 0.055 2479 Dihedral : 10.585 73.563 2325 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Rotamer: Outliers : 2.16 % Allowed : 22.32 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1697 helix: 1.65 (0.18), residues: 821 sheet: 0.21 (0.38), residues: 178 loop : -0.67 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.003 0.001 HIS B 649 PHE 0.012 0.001 PHE B 333 TYR 0.023 0.001 TYR A 305 ARG 0.013 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8334 (p0) cc_final: 0.8002 (p0) REVERT: B 75 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: B 331 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: B 360 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8649 (mptt) REVERT: B 375 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8449 (p0) REVERT: B 642 ASN cc_start: 0.8566 (t0) cc_final: 0.8332 (t0) REVERT: B 698 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8056 (mtpt) REVERT: C 6 GLU cc_start: 0.7812 (tp30) cc_final: 0.7545 (mt-10) REVERT: C 64 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7738 (mmt) REVERT: C 146 ASP cc_start: 0.6861 (p0) cc_final: 0.6400 (p0) outliers start: 33 outliers final: 15 residues processed: 209 average time/residue: 1.6905 time to fit residues: 382.0835 Evaluate side-chains 204 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 184 HIS B 413 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14773 Z= 0.278 Angle : 0.549 11.434 20071 Z= 0.284 Chirality : 0.041 0.181 2214 Planarity : 0.004 0.053 2479 Dihedral : 10.654 73.423 2325 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 2.62 % Allowed : 21.86 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1697 helix: 1.54 (0.18), residues: 823 sheet: 0.02 (0.37), residues: 194 loop : -0.68 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 368 HIS 0.004 0.001 HIS B 47 PHE 0.013 0.001 PHE B 551 TYR 0.025 0.002 TYR A 305 ARG 0.012 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5964 (OUTLIER) cc_final: 0.4404 (m110) REVERT: A 222 ASN cc_start: 0.8340 (p0) cc_final: 0.8012 (p0) REVERT: A 495 ARG cc_start: 0.8194 (ptp-110) cc_final: 0.7931 (ptm160) REVERT: B 1 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.6918 (tpt) REVERT: B 75 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7985 (mm-30) REVERT: B 331 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: B 375 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8462 (p0) REVERT: B 744 MET cc_start: 0.7051 (mmm) cc_final: 0.6719 (mmt) REVERT: C 6 GLU cc_start: 0.7837 (tp30) cc_final: 0.7586 (mt-10) REVERT: C 64 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: C 65 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: C 146 ASP cc_start: 0.6728 (p0) cc_final: 0.6341 (p0) outliers start: 40 outliers final: 22 residues processed: 210 average time/residue: 1.5968 time to fit residues: 361.7357 Evaluate side-chains 211 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 413 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14773 Z= 0.206 Angle : 0.517 11.975 20071 Z= 0.267 Chirality : 0.039 0.178 2214 Planarity : 0.004 0.053 2479 Dihedral : 10.590 73.396 2325 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 2.55 % Allowed : 21.99 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1697 helix: 1.64 (0.18), residues: 821 sheet: 0.20 (0.37), residues: 190 loop : -0.63 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE A 520 TYR 0.024 0.001 TYR A 305 ARG 0.009 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.6023 (OUTLIER) cc_final: 0.4318 (m110) REVERT: A 222 ASN cc_start: 0.8330 (p0) cc_final: 0.7996 (p0) REVERT: A 495 ARG cc_start: 0.8177 (ptp-110) cc_final: 0.7938 (ptm160) REVERT: B 1 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.6998 (tpt) REVERT: B 75 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: B 331 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: B 375 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8446 (p0) REVERT: B 642 ASN cc_start: 0.8591 (t0) cc_final: 0.8361 (t0) REVERT: B 698 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8088 (mtpt) REVERT: B 744 MET cc_start: 0.7147 (mmm) cc_final: 0.6864 (mmt) REVERT: C 6 GLU cc_start: 0.7810 (tp30) cc_final: 0.7554 (mt-10) REVERT: C 64 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7800 (mmt) REVERT: C 65 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7970 (pt0) REVERT: C 146 ASP cc_start: 0.6458 (p0) cc_final: 0.6198 (p0) outliers start: 39 outliers final: 24 residues processed: 218 average time/residue: 1.6255 time to fit residues: 382.0277 Evaluate side-chains 215 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 153 optimal weight: 0.0050 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 413 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14773 Z= 0.219 Angle : 0.533 12.343 20071 Z= 0.274 Chirality : 0.040 0.175 2214 Planarity : 0.004 0.053 2479 Dihedral : 10.590 73.373 2325 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.36 % Allowed : 22.32 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1697 helix: 1.60 (0.18), residues: 822 sheet: 0.12 (0.37), residues: 195 loop : -0.58 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE A 520 TYR 0.025 0.002 TYR A 305 ARG 0.009 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.4350 (m110) REVERT: A 182 MET cc_start: 0.4071 (ppp) cc_final: 0.3730 (ppp) REVERT: A 222 ASN cc_start: 0.8332 (p0) cc_final: 0.7999 (p0) REVERT: A 495 ARG cc_start: 0.8173 (ptp-110) cc_final: 0.7942 (ptm160) REVERT: B 1 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6927 (tpt) REVERT: B 56 THR cc_start: 0.9136 (m) cc_final: 0.8886 (p) REVERT: B 75 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: B 331 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: B 375 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8447 (p0) REVERT: B 642 ASN cc_start: 0.8592 (t0) cc_final: 0.8367 (t0) REVERT: B 698 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8088 (mtpt) REVERT: B 744 MET cc_start: 0.7118 (mmm) cc_final: 0.6859 (mmt) REVERT: C 6 GLU cc_start: 0.7808 (tp30) cc_final: 0.7558 (mt-10) REVERT: C 64 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.7793 (mmt) REVERT: C 65 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: C 146 ASP cc_start: 0.6461 (p0) cc_final: 0.6210 (p0) outliers start: 36 outliers final: 22 residues processed: 213 average time/residue: 1.5632 time to fit residues: 360.9703 Evaluate side-chains 212 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.0010 chunk 99 optimal weight: 0.7980 chunk 77 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 170 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 0.0370 overall best weight: 0.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN B 413 ASN C 13 GLN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14773 Z= 0.142 Angle : 0.493 12.802 20071 Z= 0.251 Chirality : 0.037 0.171 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.421 73.425 2325 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 1.31 % Allowed : 23.23 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1697 helix: 1.77 (0.19), residues: 819 sheet: 0.39 (0.38), residues: 184 loop : -0.49 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.004 0.001 HIS A 510 PHE 0.014 0.001 PHE B 333 TYR 0.022 0.001 TYR A 305 ARG 0.009 0.000 ARG A 495 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.6032 (OUTLIER) cc_final: 0.4335 (m110) REVERT: A 182 MET cc_start: 0.4261 (ppp) cc_final: 0.3888 (ppp) REVERT: B 1 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7021 (tpt) REVERT: B 75 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: B 331 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: B 375 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (p0) REVERT: C 6 GLU cc_start: 0.7835 (tp30) cc_final: 0.7621 (mm-30) REVERT: C 22 LYS cc_start: 0.8505 (tttm) cc_final: 0.8295 (tttp) REVERT: C 28 MET cc_start: 0.8482 (ttp) cc_final: 0.8200 (mtp) REVERT: C 65 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7960 (pt0) outliers start: 20 outliers final: 11 residues processed: 206 average time/residue: 1.7895 time to fit residues: 397.0194 Evaluate side-chains 208 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 125 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 119 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 413 ASN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100035 restraints weight = 17497.076| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.58 r_work: 0.2951 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14773 Z= 0.166 Angle : 0.513 12.542 20071 Z= 0.261 Chirality : 0.038 0.172 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.430 73.419 2325 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.37 % Allowed : 23.23 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1697 helix: 1.76 (0.19), residues: 820 sheet: 0.38 (0.38), residues: 186 loop : -0.50 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.003 0.001 HIS B 649 PHE 0.011 0.001 PHE B 333 TYR 0.023 0.001 TYR A 305 ARG 0.012 0.000 ARG A 495 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6254.45 seconds wall clock time: 110 minutes 17.04 seconds (6617.04 seconds total)