Starting phenix.real_space_refine on Fri Aug 7 15:31:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9u_40249/08_2026/8s9u_40249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9u_40249/08_2026/8s9u_40249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9u_40249/08_2026/8s9u_40249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9u_40249/08_2026/8s9u_40249.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9u_40249/08_2026/8s9u_40249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9u_40249/08_2026/8s9u_40249.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 0.074 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 69 5.49 5 S 51 5.16 5 C 14002 2.51 5 N 3989 2.21 5 O 4493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22604 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5995 Classifications: {'peptide': 768} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4268 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 525} Chain breaks: 2 Chain: "D" Number of atoms: 3967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3967 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 25, 'TRANS': 492} Chain: "E" Number of atoms: 5455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5455 Classifications: {'peptide': 678} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 634} Chain breaks: 1 Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 18} Chain: "G" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 696 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 17} Link IDs: {'rna2p': 7, 'rna3p': 25} Time building chain proxies: 4.35, per 1000 atoms: 0.19 Number of scatterers: 22604 At special positions: 0 Unit cell: (106.92, 118.26, 187.92, 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 51 16.00 P 69 15.00 O 4493 8.00 N 3989 7.00 C 14002 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: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4934 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 37 sheets defined 36.6% alpha, 21.3% beta 22 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 40 through 60 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.638A pdb=" N GLN A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 167 through 184 Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.759A pdb=" N GLY A 195 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.945A pdb=" N ILE A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 562 through 573 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 624 through 649 Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 689 through 703 removed outlier: 3.635A pdb=" N VAL A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.648A pdb=" N TRP A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 726 Processing helix chain 'A' and resid 726 through 735 removed outlier: 4.213A pdb=" N ILE A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.597A pdb=" N THR A 742 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 780 removed outlier: 6.007A pdb=" N ALA A 757 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 20 through 35 removed outlier: 3.952A pdb=" N THR C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 60 through 66 removed outlier: 4.176A pdb=" N PHE C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 Processing helix chain 'C' and resid 135 through 155 removed outlier: 4.032A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 212 removed outlier: 4.038A pdb=" N LYS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 228 Processing helix chain 'C' and resid 243 through 255 removed outlier: 5.546A pdb=" N GLU C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 removed outlier: 3.521A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 318 through 337 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.731A pdb=" N VAL C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.888A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 459 through 472 removed outlier: 3.865A pdb=" N LEU C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 removed outlier: 4.024A pdb=" N TYR C 494 " --> pdb=" O ARG C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 506 Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.735A pdb=" N PHE C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 545 through 547 No H-bonds generated for 'chain 'C' and resid 545 through 547' Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.702A pdb=" N ILE D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 161 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 206 through 214 removed outlier: 3.737A pdb=" N LEU D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 284 Processing helix chain 'D' and resid 291 through 297 removed outlier: 3.712A pdb=" N ARG D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 339 through 348 removed outlier: 3.562A pdb=" N LYS D 344 " --> pdb=" O PRO D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 369 through 375 Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 430 through 447 removed outlier: 4.575A pdb=" N ALA D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 483 Processing helix chain 'D' and resid 495 through 512 removed outlier: 3.626A pdb=" N ASP D 512 " --> pdb=" O GLU D 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 removed outlier: 3.979A pdb=" N LEU E 133 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.532A pdb=" N GLU E 171 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 210 Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 260 through 264 removed outlier: 4.059A pdb=" N ASN E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 394 removed outlier: 4.058A pdb=" N HIS E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 400 Processing helix chain 'E' and resid 414 through 419 removed outlier: 3.555A pdb=" N ILE E 418 " --> pdb=" O SER E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 466 Processing helix chain 'E' and resid 475 through 479 removed outlier: 4.029A pdb=" N LEU E 479 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 536 through 540 Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 590 through 594 removed outlier: 4.149A pdb=" N GLN E 593 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 599 Processing helix chain 'E' and resid 641 through 652 Processing helix chain 'E' and resid 665 through 669 Processing helix chain 'E' and resid 687 through 694 Processing helix chain 'E' and resid 704 through 707 Processing helix chain 'E' and resid 708 through 724 Processing helix chain 'E' and resid 732 through 744 Processing helix chain 'E' and resid 766 through 776 removed outlier: 4.059A pdb=" N PHE E 770 " --> pdb=" O ALA E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 787 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.810A pdb=" N ILE A 4 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 130 removed outlier: 6.009A pdb=" N PHE A 141 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 6.823A pdb=" N THR A 412 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA6, first strand: chain 'A' and resid 261 through 265 removed outlier: 6.658A pdb=" N GLU A 270 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 264 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 269 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A 407 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N CYS A 271 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.507A pdb=" N TYR A 360 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.641A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.641A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 529 Processing sheet with id=AB3, first strand: chain 'A' and resid 532 through 533 removed outlier: 3.654A pdb=" N LEU A 538 " --> pdb=" O GLN A 533 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 661 through 663 Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.799A pdb=" N ASN B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY B 92 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 123 removed outlier: 3.605A pdb=" N THR B 116 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 189 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU B 168 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU B 187 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR B 170 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU B 185 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA B 172 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE B 183 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'C' and resid 82 through 88 removed outlier: 6.156A pdb=" N ILE C 93 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA C 87 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 180 through 183 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.619A pdb=" N THR C 311 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU C 305 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C 354 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA C 355 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ASP C 406 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA C 357 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AC3, first strand: chain 'D' and resid 45 through 46 removed outlier: 6.418A pdb=" N VAL D 93 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 135 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 46 removed outlier: 6.418A pdb=" N VAL D 93 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 135 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG D 8 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER D 185 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS D 10 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU D 183 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR D 12 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU D 181 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU D 183 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 103 through 110 removed outlier: 10.989A pdb=" N GLU D 103 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N SER D 124 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N ARG D 105 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N LYS D 122 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N GLY D 107 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N GLY D 120 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY D 109 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 171 through 172 removed outlier: 4.767A pdb=" N GLN D 412 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN D 467 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN D 229 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL D 465 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 251 through 253 removed outlier: 4.202A pdb=" N PHE D 260 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU D 336 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N ILE D 262 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N SER D 334 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AC9, first strand: chain 'D' and resid 378 through 383 Processing sheet with id=AD1, first strand: chain 'E' and resid 750 through 751 removed outlier: 3.821A pdb=" N SER E 750 " --> pdb=" O ASN E 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AD3, first strand: chain 'E' and resid 501 through 508 removed outlier: 5.777A pdb=" N LEU E 501 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR E 638 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE E 503 " --> pdb=" O ASP E 636 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP E 636 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER E 505 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU E 634 " --> pdb=" O SER E 505 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR E 149 " --> pdb=" O ASN E 639 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N SER E 150 " --> pdb=" O THR E 682 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N THR E 682 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N ARG E 152 " --> pdb=" O ASP E 680 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASP E 680 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA E 154 " --> pdb=" O ASP E 678 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 172 through 174 removed outlier: 4.531A pdb=" N ARG E 619 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AD6, first strand: chain 'E' and resid 371 through 374 removed outlier: 3.686A pdb=" N ASN E 447 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS E 437 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ILE E 445 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU E 439 " --> pdb=" O TYR E 443 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 268 through 272 removed outlier: 7.430A pdb=" N ALA E 268 " --> pdb=" O TRP E 310 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL E 312 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TRP E 270 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN E 314 " --> pdb=" O TRP E 270 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N ALA E 316 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 298 " --> pdb=" O ARG E 313 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE E 315 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG E 296 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG E 317 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N HIS E 294 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL E 340 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N THR E 303 " --> pdb=" O THR E 338 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR E 338 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 362 " --> pdb=" O TYR E 349 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 487 through 489 Processing sheet with id=AD9, first strand: chain 'E' and resid 514 through 516 removed outlier: 3.547A pdb=" N TRP E 624 " --> pdb=" O ASP E 515 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 541 through 542 907 hydrogen bonds defined for protein. 2487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4376 1.32 - 1.44: 5887 1.44 - 1.57: 12735 1.57 - 1.69: 136 1.69 - 1.81: 74 Bond restraints: 23208 Sorted by residual: bond pdb=" C5 A F 18 " pdb=" C4 A F 18 " ideal model delta sigma weight residual 1.383 1.356 0.027 7.00e-03 2.04e+04 1.44e+01 bond pdb=" N9 A F 18 " pdb=" C4 A F 18 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.33e+01 bond pdb=" N9 A F 22 " pdb=" C4 A F 22 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.29e+01 bond pdb=" N1 U F 3 " pdb=" C2 U F 3 " ideal model delta sigma weight residual 1.381 1.350 0.031 9.00e-03 1.23e+04 1.22e+01 bond pdb=" C4 C F 8 " pdb=" C5 C F 8 " ideal model delta sigma weight residual 1.425 1.398 0.027 8.00e-03 1.56e+04 1.15e+01 ... (remaining 23203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 30601 2.28 - 4.55: 1030 4.55 - 6.83: 104 6.83 - 9.11: 16 9.11 - 11.38: 6 Bond angle restraints: 31757 Sorted by residual: angle pdb=" O5' U F 32 " pdb=" C5' U F 32 " pdb=" C4' U F 32 " ideal model delta sigma weight residual 109.40 117.48 -8.08 8.00e-01 1.56e+00 1.02e+02 angle pdb=" O5' C F 2 " pdb=" C5' C F 2 " pdb=" C4' C F 2 " ideal model delta sigma weight residual 109.40 115.26 -5.86 8.00e-01 1.56e+00 5.37e+01 angle pdb=" O5' C G 26 " pdb=" C5' C G 26 " pdb=" C4' C G 26 " ideal model delta sigma weight residual 109.40 115.06 -5.66 8.00e-01 1.56e+00 5.00e+01 angle pdb=" O5' C F 30 " pdb=" C5' C F 30 " pdb=" C4' C F 30 " ideal model delta sigma weight residual 109.40 114.99 -5.59 8.00e-01 1.56e+00 4.89e+01 angle pdb=" O4' G F 27 " pdb=" C1' G F 27 " pdb=" N9 G F 27 " ideal model delta sigma weight residual 108.20 113.07 -4.87 8.00e-01 1.56e+00 3.70e+01 ... (remaining 31752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 13626 35.80 - 71.61: 355 71.61 - 107.41: 59 107.41 - 143.22: 4 143.22 - 179.02: 3 Dihedral angle restraints: 14047 sinusoidal: 6350 harmonic: 7697 Sorted by residual: dihedral pdb=" O4' C F 2 " pdb=" C1' C F 2 " pdb=" N1 C F 2 " pdb=" C2 C F 2 " ideal model delta sinusoidal sigma weight residual -128.00 49.28 -177.28 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 14 " pdb=" C1' U F 14 " pdb=" N1 U F 14 " pdb=" C2 U F 14 " ideal model delta sinusoidal sigma weight residual -128.00 43.89 -171.89 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA VAL A 16 " pdb=" C VAL A 16 " pdb=" N GLY A 17 " pdb=" CA GLY A 17 " ideal model delta harmonic sigma weight residual 180.00 144.63 35.37 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 14044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2493 0.062 - 0.124: 867 0.124 - 0.186: 159 0.186 - 0.247: 22 0.247 - 0.309: 3 Chirality restraints: 3544 Sorted by residual: chirality pdb=" C3' G G 24 " pdb=" C4' G G 24 " pdb=" O3' G G 24 " pdb=" C2' G G 24 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG C 436 " pdb=" N ARG C 436 " pdb=" C ARG C 436 " pdb=" CB ARG C 436 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C4' G G 24 " pdb=" C5' G G 24 " pdb=" O4' G G 24 " pdb=" C3' G G 24 " both_signs ideal model delta sigma weight residual False -2.50 -2.24 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3541 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 19 " 0.059 2.00e-02 2.50e+03 3.67e-02 3.03e+01 pdb=" N1 C F 19 " -0.090 2.00e-02 2.50e+03 pdb=" C2 C F 19 " 0.017 2.00e-02 2.50e+03 pdb=" O2 C F 19 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C F 19 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C F 19 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C F 19 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C F 19 " 0.006 2.00e-02 2.50e+03 pdb=" C6 C F 19 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 126 " 0.109 9.50e-02 1.11e+02 6.21e-02 2.00e+01 pdb=" NE ARG E 126 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG E 126 " 0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG E 126 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG E 126 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 419 " 0.113 9.50e-02 1.11e+02 6.20e-02 1.77e+01 pdb=" NE ARG D 419 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG D 419 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG D 419 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG D 419 " -0.019 2.00e-02 2.50e+03 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 487 2.66 - 3.22: 21807 3.22 - 3.78: 37289 3.78 - 4.34: 54830 4.34 - 4.90: 87719 Nonbonded interactions: 202132 Sorted by model distance: nonbonded pdb=" OE2 GLU B 99 " pdb=" OH TYR B 170 " model vdw 2.099 3.040 nonbonded pdb=" O ASP A 140 " pdb=" O2' C G 44 " model vdw 2.135 3.040 nonbonded pdb=" NH2 ARG A 489 " pdb=" OE1 GLN B 112 " model vdw 2.155 3.120 nonbonded pdb=" OD2 ASP D 162 " pdb=" OH TYR D 216 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLN E 287 " pdb=" NH2 ARG E 317 " model vdw 2.197 3.120 ... (remaining 202127 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=0.00 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: 7.650 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: 0.470 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.330 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.010 0.117 23208 Z= 0.515 Angle : 0.945 11.382 31757 Z= 0.576 Chirality : 0.062 0.309 3544 Planarity : 0.007 0.064 3898 Dihedral : 16.422 179.022 9113 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.68 % Favored : 96.02 % Rotamer: Outliers : 1.33 % Allowed : 5.66 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2664 helix: -1.55 (0.15), residues: 834 sheet: -0.05 (0.23), residues: 474 loop : -0.61 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.009 ARG E 126 TYR 0.032 0.005 TYR A 279 PHE 0.029 0.003 PHE E 633 TRP 0.046 0.004 TRP D 388 HIS 0.012 0.003 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.01012 / 0.52 (23208) covalent geometry : angle 0.94471 / 0.58 (31757) hydrogen bonds : bond 0.19271 / 13.24 ( 947) hydrogen bonds : angle 8.21986 / 5.90 ( 2593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 425 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 THR cc_start: 0.8709 (m) cc_final: 0.8437 (p) REVERT: A 694 THR cc_start: 0.8309 (m) cc_final: 0.8001 (p) REVERT: C 81 ASP cc_start: 0.6659 (p0) cc_final: 0.6230 (t0) REVERT: C 309 ASP cc_start: 0.7225 (t0) cc_final: 0.6365 (m-30) REVERT: C 351 ASP cc_start: 0.7651 (p0) cc_final: 0.7425 (m-30) REVERT: C 362 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.5877 (pt) REVERT: C 374 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5940 (tt) REVERT: C 420 ARG cc_start: 0.6689 (mpt180) cc_final: 0.5411 (mtm180) REVERT: C 478 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.6079 (mmmt) REVERT: C 509 GLN cc_start: 0.7651 (mm110) cc_final: 0.7152 (pm20) REVERT: C 515 LYS cc_start: 0.8654 (mttt) cc_final: 0.8335 (mttp) REVERT: D 235 MET cc_start: 0.9114 (ptm) cc_final: 0.8907 (ppp) REVERT: D 241 ASP cc_start: 0.6820 (m-30) cc_final: 0.6555 (m-30) REVERT: E 245 ILE cc_start: 0.8279 (pp) cc_final: 0.7977 (mt) REVERT: E 266 MET cc_start: 0.8443 (mmt) cc_final: 0.8187 (mmm) REVERT: E 548 ILE cc_start: 0.8615 (mm) cc_final: 0.8306 (mm) outliers start: 30 outliers final: 7 residues processed: 452 average time/residue: 0.6661 time to fit residues: 338.2238 Evaluate side-chains 237 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 227 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain E residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 493 ASN A 745 GLN A 750 GLN B 120 GLN C 435 ASN D 362 GLN D 414 HIS E 174 ASN E 287 GLN E 320 GLN E 354 ASN E 425 ASN E 617 GLN E 731 GLN E 788 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089602 restraints weight = 34925.953| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.90 r_work: 0.3017 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23208 Z= 0.176 Angle : 0.686 10.910 31757 Z= 0.368 Chirality : 0.047 0.444 3544 Planarity : 0.005 0.065 3898 Dihedral : 15.241 179.036 3986 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.18 % Favored : 97.67 % Rotamer: Outliers : 3.32 % Allowed : 11.58 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2664 helix: 0.15 (0.17), residues: 845 sheet: -0.07 (0.24), residues: 460 loop : -0.03 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 377 TYR 0.022 0.002 TYR C 267 PHE 0.017 0.002 PHE E 734 TRP 0.019 0.002 TRP A 14 HIS 0.008 0.001 HIS D 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (23208) covalent geometry : angle 0.68644 / 0.37 (31757) hydrogen bonds : bond 0.05173 / 3.53 ( 947) hydrogen bonds : angle 5.93519 / 4.19 ( 2593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 259 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.6366 (mmt) REVERT: A 24 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.4842 (mm-30) REVERT: A 469 THR cc_start: 0.8790 (m) cc_final: 0.8499 (p) REVERT: A 488 ASP cc_start: 0.8131 (p0) cc_final: 0.7660 (p0) REVERT: A 694 THR cc_start: 0.7841 (m) cc_final: 0.7631 (p) REVERT: B 78 LEU cc_start: 0.8928 (mm) cc_final: 0.8586 (tp) REVERT: B 116 THR cc_start: 0.8915 (t) cc_final: 0.8676 (p) REVERT: B 171 ILE cc_start: 0.8641 (mt) cc_final: 0.8406 (mp) REVERT: C 81 ASP cc_start: 0.7037 (p0) cc_final: 0.6224 (t0) REVERT: C 211 ARG cc_start: 0.7920 (tmm160) cc_final: 0.7450 (ttp80) REVERT: C 223 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6773 (tm-30) REVERT: C 309 ASP cc_start: 0.7125 (t0) cc_final: 0.6077 (m-30) REVERT: C 351 ASP cc_start: 0.7690 (p0) cc_final: 0.7077 (m-30) REVERT: C 362 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6113 (pt) REVERT: C 374 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5395 (tt) REVERT: C 420 ARG cc_start: 0.6016 (mpt180) cc_final: 0.4760 (mtm180) REVERT: C 478 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5724 (mmmt) REVERT: C 509 GLN cc_start: 0.7659 (mm110) cc_final: 0.6840 (pm20) REVERT: C 515 LYS cc_start: 0.8468 (mttt) cc_final: 0.8161 (mttp) REVERT: C 530 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: D 4 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7739 (tmtm) REVERT: D 101 ASP cc_start: 0.7975 (t0) cc_final: 0.7737 (t70) REVERT: D 241 ASP cc_start: 0.7170 (m-30) cc_final: 0.6955 (m-30) REVERT: D 297 ARG cc_start: 0.8574 (ptp-110) cc_final: 0.8362 (mtm110) REVERT: D 318 ASP cc_start: 0.7746 (t0) cc_final: 0.7498 (t0) REVERT: D 480 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: D 486 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8610 (mtm) REVERT: E 136 CYS cc_start: 0.8947 (t) cc_final: 0.8532 (m) REVERT: E 245 ILE cc_start: 0.8298 (pp) cc_final: 0.7996 (mt) REVERT: E 266 MET cc_start: 0.8961 (mmt) cc_final: 0.8657 (mmm) REVERT: E 314 GLN cc_start: 0.8682 (tt0) cc_final: 0.8441 (tt0) REVERT: E 330 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7594 (ptm160) REVERT: E 354 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8002 (m110) REVERT: E 467 ASP cc_start: 0.8197 (t70) cc_final: 0.7977 (m-30) REVERT: E 630 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: E 763 ASP cc_start: 0.8124 (m-30) cc_final: 0.7653 (m-30) outliers start: 75 outliers final: 18 residues processed: 307 average time/residue: 0.5928 time to fit residues: 205.6430 Evaluate side-chains 247 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 630 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 121 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 244 optimal weight: 0.0070 chunk 263 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 112 GLN A 622 HIS A 733 HIS A 745 GLN A 750 GLN B 120 GLN D 119 ASN D 348 ASN D 362 GLN E 262 ASN E 320 GLN E 354 ASN E 425 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087904 restraints weight = 35096.479| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.16 r_work: 0.2995 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23208 Z= 0.182 Angle : 0.629 11.519 31757 Z= 0.336 Chirality : 0.045 0.416 3544 Planarity : 0.005 0.061 3898 Dihedral : 14.923 179.269 3977 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.67 % Favored : 97.18 % Rotamer: Outliers : 2.70 % Allowed : 14.10 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2664 helix: 0.53 (0.17), residues: 851 sheet: -0.11 (0.24), residues: 452 loop : 0.08 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 315 TYR 0.015 0.001 TYR E 724 PHE 0.016 0.002 PHE E 734 TRP 0.014 0.002 TRP D 388 HIS 0.007 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (23208) covalent geometry : angle 0.62887 / 0.34 (31757) hydrogen bonds : bond 0.04704 / 3.19 ( 947) hydrogen bonds : angle 5.55343 / 3.90 ( 2593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 239 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.6276 (mmt) REVERT: A 24 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4816 (mm-30) REVERT: A 145 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 200 GLU cc_start: 0.8818 (tt0) cc_final: 0.8533 (tt0) REVERT: A 469 THR cc_start: 0.8787 (m) cc_final: 0.8497 (p) REVERT: A 488 ASP cc_start: 0.8051 (p0) cc_final: 0.7600 (p0) REVERT: A 694 THR cc_start: 0.7959 (m) cc_final: 0.7606 (p) REVERT: A 727 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: A 750 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: B 78 LEU cc_start: 0.8951 (mm) cc_final: 0.8614 (tp) REVERT: B 98 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8346 (m) REVERT: B 116 THR cc_start: 0.8936 (t) cc_final: 0.8703 (p) REVERT: B 171 ILE cc_start: 0.8648 (mt) cc_final: 0.8413 (mp) REVERT: C 81 ASP cc_start: 0.6960 (p0) cc_final: 0.6228 (t0) REVERT: C 146 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7779 (ptmt) REVERT: C 211 ARG cc_start: 0.7926 (tmm160) cc_final: 0.7488 (ttp80) REVERT: C 220 ASP cc_start: 0.5697 (t0) cc_final: 0.5426 (t70) REVERT: C 223 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6774 (tm-30) REVERT: C 309 ASP cc_start: 0.6896 (t0) cc_final: 0.5862 (m-30) REVERT: C 351 ASP cc_start: 0.7764 (p0) cc_final: 0.7090 (m-30) REVERT: C 362 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6246 (pt) REVERT: C 374 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5332 (tt) REVERT: C 420 ARG cc_start: 0.6004 (mpt180) cc_final: 0.4718 (mtm180) REVERT: C 509 GLN cc_start: 0.7685 (mm110) cc_final: 0.6897 (pm20) REVERT: C 515 LYS cc_start: 0.8438 (mttt) cc_final: 0.8117 (mttp) REVERT: D 4 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7786 (tmtm) REVERT: D 101 ASP cc_start: 0.7919 (t0) cc_final: 0.7687 (t0) REVERT: D 241 ASP cc_start: 0.7233 (m-30) cc_final: 0.7031 (m-30) REVERT: D 297 ARG cc_start: 0.8656 (ptp-110) cc_final: 0.8377 (mtm110) REVERT: D 471 ASN cc_start: 0.8490 (t0) cc_final: 0.8283 (t0) REVERT: D 480 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: E 136 CYS cc_start: 0.8933 (t) cc_final: 0.8582 (m) REVERT: E 266 MET cc_start: 0.8917 (mmt) cc_final: 0.8660 (mmm) REVERT: E 304 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7786 (ttt-90) REVERT: E 314 GLN cc_start: 0.8667 (tt0) cc_final: 0.8442 (tt0) REVERT: E 330 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7793 (ptm160) REVERT: E 428 ASP cc_start: 0.8540 (t0) cc_final: 0.8320 (t0) REVERT: E 467 ASP cc_start: 0.8228 (t70) cc_final: 0.8010 (m-30) REVERT: E 468 GLU cc_start: 0.8381 (tp30) cc_final: 0.8000 (tp30) REVERT: E 551 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: E 763 ASP cc_start: 0.8063 (m-30) cc_final: 0.7611 (m-30) outliers start: 61 outliers final: 20 residues processed: 281 average time/residue: 0.6505 time to fit residues: 205.6343 Evaluate side-chains 247 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 750 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 594 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 260 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 112 GLN B 66 ASN B 120 GLN C 59 ASN C 246 GLN D 362 GLN E 287 GLN E 320 GLN E 354 ASN E 536 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089330 restraints weight = 35113.828| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.73 r_work: 0.2928 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23208 Z= 0.215 Angle : 0.627 11.611 31757 Z= 0.332 Chirality : 0.046 0.408 3544 Planarity : 0.005 0.064 3898 Dihedral : 14.802 178.679 3973 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 3.63 % Allowed : 14.24 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2664 helix: 0.59 (0.17), residues: 853 sheet: -0.37 (0.24), residues: 460 loop : 0.14 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 377 TYR 0.015 0.002 TYR E 724 PHE 0.017 0.002 PHE E 734 TRP 0.015 0.002 TRP D 388 HIS 0.005 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (23208) covalent geometry : angle 0.62740 / 0.33 (31757) hydrogen bonds : bond 0.04448 / 3.03 ( 947) hydrogen bonds : angle 5.43397 / 3.81 ( 2593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 227 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.6370 (mmt) REVERT: A 24 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.4794 (mm-30) REVERT: A 145 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: A 198 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8371 (ttp-170) REVERT: A 200 GLU cc_start: 0.8661 (tt0) cc_final: 0.8406 (tt0) REVERT: A 469 THR cc_start: 0.8814 (m) cc_final: 0.8510 (p) REVERT: A 488 ASP cc_start: 0.7919 (p0) cc_final: 0.7510 (p0) REVERT: A 638 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: A 694 THR cc_start: 0.7974 (m) cc_final: 0.7588 (p) REVERT: A 727 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: B 78 LEU cc_start: 0.8940 (mm) cc_final: 0.8590 (tp) REVERT: B 98 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8323 (m) REVERT: B 116 THR cc_start: 0.8933 (t) cc_final: 0.8711 (p) REVERT: B 171 ILE cc_start: 0.8636 (mt) cc_final: 0.8395 (mp) REVERT: C 81 ASP cc_start: 0.6864 (p0) cc_final: 0.6235 (t0) REVERT: C 188 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: C 211 ARG cc_start: 0.7882 (tmm160) cc_final: 0.7486 (ttp80) REVERT: C 220 ASP cc_start: 0.5620 (t0) cc_final: 0.5396 (t70) REVERT: C 223 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 246 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7647 (tm130) REVERT: C 249 LEU cc_start: 0.8418 (mt) cc_final: 0.7976 (pp) REVERT: C 309 ASP cc_start: 0.6868 (t0) cc_final: 0.5787 (m-30) REVERT: C 351 ASP cc_start: 0.7743 (p0) cc_final: 0.7149 (m-30) REVERT: C 417 ASP cc_start: 0.7255 (t0) cc_final: 0.6918 (t0) REVERT: C 420 ARG cc_start: 0.6098 (mpt180) cc_final: 0.4790 (mtm180) REVERT: C 509 GLN cc_start: 0.7700 (mm110) cc_final: 0.6857 (pm20) REVERT: C 515 LYS cc_start: 0.8441 (mttt) cc_final: 0.8143 (mttp) REVERT: C 530 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: D 4 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7751 (tmtm) REVERT: D 101 ASP cc_start: 0.7905 (t0) cc_final: 0.7680 (t0) REVERT: D 241 ASP cc_start: 0.7139 (m-30) cc_final: 0.6905 (m-30) REVERT: D 338 MET cc_start: 0.8105 (mtm) cc_final: 0.7794 (ptp) REVERT: D 471 ASN cc_start: 0.8374 (t0) cc_final: 0.8153 (t0) REVERT: D 480 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: E 136 CYS cc_start: 0.8823 (t) cc_final: 0.8553 (m) REVERT: E 231 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8361 (mpp) REVERT: E 245 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7848 (mt) REVERT: E 266 MET cc_start: 0.8845 (mmp) cc_final: 0.8533 (mmm) REVERT: E 304 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7614 (tpt-90) REVERT: E 314 GLN cc_start: 0.8571 (tt0) cc_final: 0.8323 (tt0) REVERT: E 317 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7546 (mtm-85) REVERT: E 330 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7778 (ptm160) REVERT: E 343 GLN cc_start: 0.8652 (tt0) cc_final: 0.8398 (tm-30) REVERT: E 359 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.7197 (m-70) REVERT: E 452 MET cc_start: 0.9035 (mtp) cc_final: 0.8711 (mtt) REVERT: E 551 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: E 763 ASP cc_start: 0.8036 (m-30) cc_final: 0.7615 (m-30) outliers start: 82 outliers final: 31 residues processed: 285 average time/residue: 0.6840 time to fit residues: 220.4120 Evaluate side-chains 266 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 191 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 112 GLN A 712 ASN ** A 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS B 66 ASN B 120 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN C 242 ASN D 113 HIS D 362 GLN E 320 GLN E 425 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090245 restraints weight = 34803.479| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.89 r_work: 0.3038 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23208 Z= 0.139 Angle : 0.571 12.206 31757 Z= 0.303 Chirality : 0.043 0.392 3544 Planarity : 0.004 0.050 3898 Dihedral : 14.719 178.437 3971 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 3.14 % Allowed : 15.65 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2664 helix: 0.85 (0.18), residues: 845 sheet: -0.44 (0.24), residues: 465 loop : 0.25 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 259 TYR 0.016 0.001 TYR A 554 PHE 0.013 0.001 PHE D 134 TRP 0.016 0.001 TRP A 532 HIS 0.005 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (23208) covalent geometry : angle 0.57073 / 0.30 (31757) hydrogen bonds : bond 0.04001 / 2.73 ( 947) hydrogen bonds : angle 5.23132 / 3.67 ( 2593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6285 (mmt) REVERT: A 24 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.4738 (mm-30) REVERT: A 145 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: A 198 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8460 (ttp-170) REVERT: A 200 GLU cc_start: 0.8756 (tt0) cc_final: 0.8501 (tt0) REVERT: A 304 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 405 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: A 469 THR cc_start: 0.8850 (m) cc_final: 0.8541 (p) REVERT: A 488 ASP cc_start: 0.7908 (p0) cc_final: 0.7374 (p0) REVERT: A 694 THR cc_start: 0.7956 (m) cc_final: 0.7553 (p) REVERT: A 712 ASN cc_start: 0.8311 (m110) cc_final: 0.7869 (t0) REVERT: A 727 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: B 26 ASP cc_start: 0.8370 (t70) cc_final: 0.8119 (t0) REVERT: B 78 LEU cc_start: 0.8942 (mm) cc_final: 0.8594 (tp) REVERT: B 87 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: B 116 THR cc_start: 0.8948 (t) cc_final: 0.8738 (p) REVERT: B 168 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 171 ILE cc_start: 0.8642 (mt) cc_final: 0.8409 (mp) REVERT: C 81 ASP cc_start: 0.6882 (p0) cc_final: 0.6234 (t0) REVERT: C 211 ARG cc_start: 0.7888 (tmm160) cc_final: 0.7459 (ttp80) REVERT: C 220 ASP cc_start: 0.5479 (t0) cc_final: 0.5258 (t70) REVERT: C 223 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6861 (tm-30) REVERT: C 226 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8030 (mtmt) REVERT: C 309 ASP cc_start: 0.6928 (t0) cc_final: 0.5883 (m-30) REVERT: C 351 ASP cc_start: 0.7777 (p0) cc_final: 0.7134 (m-30) REVERT: C 417 ASP cc_start: 0.7239 (t0) cc_final: 0.6922 (t0) REVERT: C 420 ARG cc_start: 0.5991 (mpt180) cc_final: 0.4706 (mtm180) REVERT: C 509 GLN cc_start: 0.7693 (mm110) cc_final: 0.6871 (pm20) REVERT: C 515 LYS cc_start: 0.8432 (mttt) cc_final: 0.8128 (mttp) REVERT: D 4 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7759 (tmtm) REVERT: D 101 ASP cc_start: 0.7917 (t0) cc_final: 0.7694 (t0) REVERT: D 164 ARG cc_start: 0.8450 (mmm160) cc_final: 0.8205 (mmm160) REVERT: D 175 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7738 (ttm-80) REVERT: D 338 MET cc_start: 0.7999 (mtm) cc_final: 0.7720 (ptp) REVERT: D 471 ASN cc_start: 0.8280 (t0) cc_final: 0.7731 (p0) REVERT: D 480 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: E 136 CYS cc_start: 0.8784 (t) cc_final: 0.8476 (m) REVERT: E 245 ILE cc_start: 0.8265 (pp) cc_final: 0.7866 (mt) REVERT: E 266 MET cc_start: 0.8852 (mmp) cc_final: 0.8564 (mmm) REVERT: E 314 GLN cc_start: 0.8563 (tt0) cc_final: 0.8197 (mt0) REVERT: E 330 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7798 (ptm160) REVERT: E 343 GLN cc_start: 0.8663 (tt0) cc_final: 0.8443 (tm-30) REVERT: E 345 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: E 425 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: E 452 MET cc_start: 0.9050 (mtp) cc_final: 0.8696 (mtt) REVERT: E 468 GLU cc_start: 0.8209 (tp30) cc_final: 0.7967 (tp30) REVERT: E 551 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: E 630 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8352 (tp30) REVERT: E 763 ASP cc_start: 0.8026 (m-30) cc_final: 0.7611 (m-30) outliers start: 71 outliers final: 31 residues processed: 280 average time/residue: 0.7172 time to fit residues: 227.3336 Evaluate side-chains 256 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 65 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 112 GLN ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 120 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN D 253 GLN D 362 GLN E 257 ASN E 287 GLN E 320 GLN E 425 ASN E 447 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.088694 restraints weight = 34997.017| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.93 r_work: 0.3005 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23208 Z= 0.179 Angle : 0.587 11.918 31757 Z= 0.310 Chirality : 0.044 0.397 3544 Planarity : 0.004 0.056 3898 Dihedral : 14.658 178.382 3971 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.52 % Rotamer: Outliers : 3.23 % Allowed : 16.36 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2664 helix: 0.86 (0.18), residues: 847 sheet: -0.43 (0.24), residues: 467 loop : 0.26 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 424 TYR 0.013 0.001 TYR E 573 PHE 0.015 0.002 PHE E 734 TRP 0.013 0.001 TRP D 388 HIS 0.005 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (23208) covalent geometry : angle 0.58706 / 0.31 (31757) hydrogen bonds : bond 0.04064 / 2.77 ( 947) hydrogen bonds : angle 5.19325 / 3.64 ( 2593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.6331 (mmt) REVERT: A 24 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.4712 (mm-30) REVERT: A 198 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8447 (ttp-170) REVERT: A 200 GLU cc_start: 0.8812 (tt0) cc_final: 0.8587 (tt0) REVERT: A 304 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 405 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: A 469 THR cc_start: 0.8862 (m) cc_final: 0.8534 (p) REVERT: A 694 THR cc_start: 0.7998 (m) cc_final: 0.7595 (p) REVERT: A 712 ASN cc_start: 0.8329 (m110) cc_final: 0.7986 (t0) REVERT: A 727 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: B 66 ASN cc_start: 0.8036 (m-40) cc_final: 0.7700 (m110) REVERT: B 78 LEU cc_start: 0.8950 (mm) cc_final: 0.8616 (tp) REVERT: B 116 THR cc_start: 0.8946 (t) cc_final: 0.8725 (p) REVERT: B 168 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 171 ILE cc_start: 0.8643 (mt) cc_final: 0.8404 (mp) REVERT: C 81 ASP cc_start: 0.6871 (p0) cc_final: 0.6242 (t0) REVERT: C 188 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: C 211 ARG cc_start: 0.7927 (tmm160) cc_final: 0.7501 (ttp80) REVERT: C 220 ASP cc_start: 0.5496 (t0) cc_final: 0.5256 (t70) REVERT: C 223 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6857 (tm-30) REVERT: C 226 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8012 (mtmt) REVERT: C 309 ASP cc_start: 0.6951 (t0) cc_final: 0.5897 (m-30) REVERT: C 351 ASP cc_start: 0.7782 (p0) cc_final: 0.7149 (m-30) REVERT: C 417 ASP cc_start: 0.7206 (t0) cc_final: 0.6893 (t0) REVERT: C 420 ARG cc_start: 0.5975 (mpt180) cc_final: 0.4670 (mtm180) REVERT: C 509 GLN cc_start: 0.7742 (mm110) cc_final: 0.6915 (pm20) REVERT: C 515 LYS cc_start: 0.8429 (mttt) cc_final: 0.8127 (mttp) REVERT: C 530 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7597 (tp30) REVERT: D 4 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7779 (tmtm) REVERT: D 101 ASP cc_start: 0.7925 (t0) cc_final: 0.7721 (t70) REVERT: D 338 MET cc_start: 0.8017 (mtm) cc_final: 0.7747 (ptp) REVERT: D 471 ASN cc_start: 0.8169 (t0) cc_final: 0.7710 (p0) REVERT: D 480 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: E 136 CYS cc_start: 0.8827 (t) cc_final: 0.8498 (m) REVERT: E 266 MET cc_start: 0.8847 (mmp) cc_final: 0.8574 (mmm) REVERT: E 287 GLN cc_start: 0.6015 (OUTLIER) cc_final: 0.5657 (tt0) REVERT: E 314 GLN cc_start: 0.8579 (tt0) cc_final: 0.8211 (mt0) REVERT: E 317 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7837 (mtt90) REVERT: E 330 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7822 (ptm160) REVERT: E 425 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: E 452 MET cc_start: 0.9060 (mtp) cc_final: 0.8736 (mtt) REVERT: E 468 GLU cc_start: 0.8250 (tp30) cc_final: 0.7971 (tp30) REVERT: E 519 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7841 (p0) REVERT: E 551 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: E 630 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: E 763 ASP cc_start: 0.8049 (m-30) cc_final: 0.7637 (m-30) outliers start: 73 outliers final: 33 residues processed: 270 average time/residue: 0.6782 time to fit residues: 207.1861 Evaluate side-chains 259 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 166 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 15 HIS B 120 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN D 362 GLN E 287 GLN E 394 HIS E 425 ASN E 594 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086695 restraints weight = 34856.100| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.92 r_work: 0.2973 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23208 Z= 0.233 Angle : 0.612 11.712 31757 Z= 0.322 Chirality : 0.046 0.400 3544 Planarity : 0.005 0.063 3898 Dihedral : 14.623 178.396 3971 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 3.58 % Allowed : 16.36 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2664 helix: 0.80 (0.18), residues: 847 sheet: -0.37 (0.24), residues: 460 loop : 0.20 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.014 0.002 TYR E 573 PHE 0.017 0.002 PHE E 734 TRP 0.016 0.002 TRP D 388 HIS 0.005 0.001 HIS E 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (23208) covalent geometry : angle 0.61241 / 0.32 (31757) hydrogen bonds : bond 0.04227 / 2.89 ( 947) hydrogen bonds : angle 5.24926 / 3.68 ( 2593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 219 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6299 (mmt) REVERT: A 24 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.4781 (tp30) REVERT: A 198 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8414 (ttp-170) REVERT: A 200 GLU cc_start: 0.8866 (tt0) cc_final: 0.8632 (tt0) REVERT: A 304 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 405 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: A 469 THR cc_start: 0.8876 (m) cc_final: 0.8532 (p) REVERT: A 638 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: A 694 THR cc_start: 0.7947 (m) cc_final: 0.7543 (p) REVERT: A 712 ASN cc_start: 0.8368 (m110) cc_final: 0.8018 (t0) REVERT: A 727 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: B 116 THR cc_start: 0.8946 (t) cc_final: 0.8711 (p) REVERT: B 193 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7379 (mtpm) REVERT: C 81 ASP cc_start: 0.6857 (p0) cc_final: 0.6260 (t0) REVERT: C 134 LYS cc_start: 0.7336 (pttt) cc_final: 0.7000 (mmtm) REVERT: C 188 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: C 211 ARG cc_start: 0.7916 (tmm160) cc_final: 0.7495 (ttp80) REVERT: C 223 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6851 (tm-30) REVERT: C 309 ASP cc_start: 0.6980 (t0) cc_final: 0.5894 (m-30) REVERT: C 351 ASP cc_start: 0.7808 (p0) cc_final: 0.7176 (m-30) REVERT: C 417 ASP cc_start: 0.7218 (t0) cc_final: 0.6904 (t0) REVERT: C 420 ARG cc_start: 0.6002 (mpt180) cc_final: 0.4661 (mtm180) REVERT: C 509 GLN cc_start: 0.7782 (mm110) cc_final: 0.6866 (pm20) REVERT: C 515 LYS cc_start: 0.8389 (mttt) cc_final: 0.8098 (mttp) REVERT: C 530 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: D 4 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7759 (tmtm) REVERT: D 101 ASP cc_start: 0.7964 (t0) cc_final: 0.7734 (t70) REVERT: D 338 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7818 (ptp) REVERT: D 471 ASN cc_start: 0.8187 (t0) cc_final: 0.7726 (p0) REVERT: D 480 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: E 136 CYS cc_start: 0.8891 (t) cc_final: 0.8589 (m) REVERT: E 266 MET cc_start: 0.8828 (mmp) cc_final: 0.8548 (mmm) REVERT: E 330 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7808 (ptm160) REVERT: E 425 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7875 (m-40) REVERT: E 452 MET cc_start: 0.9138 (mtp) cc_final: 0.8757 (mtt) REVERT: E 468 GLU cc_start: 0.8211 (tp30) cc_final: 0.7938 (tp30) REVERT: E 551 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: E 630 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: E 763 ASP cc_start: 0.8079 (m-30) cc_final: 0.7688 (m-30) outliers start: 81 outliers final: 46 residues processed: 277 average time/residue: 0.6374 time to fit residues: 200.7548 Evaluate side-chains 270 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 207 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 154 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN B 66 ASN B 120 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN D 330 ASN D 362 GLN E 287 GLN E 425 ASN E 519 ASN E 594 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088123 restraints weight = 34506.050| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.90 r_work: 0.2997 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23208 Z= 0.148 Angle : 0.574 12.001 31757 Z= 0.303 Chirality : 0.043 0.383 3544 Planarity : 0.004 0.055 3898 Dihedral : 14.629 178.219 3971 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.56 % Rotamer: Outliers : 3.45 % Allowed : 16.71 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2664 helix: 0.94 (0.18), residues: 847 sheet: -0.50 (0.24), residues: 479 loop : 0.28 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 82 TYR 0.014 0.001 TYR E 573 PHE 0.014 0.001 PHE E 734 TRP 0.014 0.001 TRP A 14 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (23208) covalent geometry : angle 0.57402 / 0.30 (31757) hydrogen bonds : bond 0.03924 / 2.68 ( 947) hydrogen bonds : angle 5.17074 / 3.62 ( 2593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 208 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6348 (mmt) REVERT: A 24 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.4791 (tp30) REVERT: A 145 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: A 198 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8400 (ttp-170) REVERT: A 200 GLU cc_start: 0.8835 (tt0) cc_final: 0.8620 (tt0) REVERT: A 304 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8646 (mp) REVERT: A 405 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: A 432 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8751 (mppt) REVERT: A 501 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7993 (tttt) REVERT: A 694 THR cc_start: 0.7948 (m) cc_final: 0.7557 (p) REVERT: A 712 ASN cc_start: 0.8343 (m110) cc_final: 0.7992 (t0) REVERT: B 66 ASN cc_start: 0.8040 (m-40) cc_final: 0.7680 (m-40) REVERT: B 78 LEU cc_start: 0.8935 (mm) cc_final: 0.8601 (tp) REVERT: B 116 THR cc_start: 0.8961 (t) cc_final: 0.8727 (p) REVERT: C 81 ASP cc_start: 0.6855 (p0) cc_final: 0.6290 (t0) REVERT: C 83 GLU cc_start: 0.8022 (tt0) cc_final: 0.7779 (tm-30) REVERT: C 152 ARG cc_start: 0.7181 (ttm110) cc_final: 0.6926 (ttp80) REVERT: C 188 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: C 211 ARG cc_start: 0.7916 (tmm160) cc_final: 0.7488 (ttp80) REVERT: C 223 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6905 (tm-30) REVERT: C 309 ASP cc_start: 0.6951 (t0) cc_final: 0.5888 (m-30) REVERT: C 351 ASP cc_start: 0.7776 (p0) cc_final: 0.7191 (m-30) REVERT: C 417 ASP cc_start: 0.7233 (t0) cc_final: 0.6914 (t0) REVERT: C 420 ARG cc_start: 0.5973 (mpt180) cc_final: 0.4627 (mtm180) REVERT: C 509 GLN cc_start: 0.7778 (mm110) cc_final: 0.6872 (pm20) REVERT: C 515 LYS cc_start: 0.8404 (mttt) cc_final: 0.8111 (mttp) REVERT: D 4 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7802 (tmtm) REVERT: D 101 ASP cc_start: 0.7894 (t0) cc_final: 0.7686 (t70) REVERT: D 338 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7760 (ptp) REVERT: D 471 ASN cc_start: 0.8098 (t0) cc_final: 0.7774 (p0) REVERT: D 480 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: E 136 CYS cc_start: 0.8837 (t) cc_final: 0.8503 (m) REVERT: E 266 MET cc_start: 0.8817 (mmp) cc_final: 0.8560 (mmm) REVERT: E 314 GLN cc_start: 0.8503 (tt0) cc_final: 0.8156 (mt0) REVERT: E 317 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7685 (mtm-85) REVERT: E 330 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7802 (ptm160) REVERT: E 425 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8059 (m-40) REVERT: E 452 MET cc_start: 0.9116 (mtp) cc_final: 0.8781 (mtt) REVERT: E 468 GLU cc_start: 0.8222 (tp30) cc_final: 0.7942 (tp30) REVERT: E 630 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8430 (tp30) outliers start: 78 outliers final: 33 residues processed: 268 average time/residue: 0.6871 time to fit residues: 208.7218 Evaluate side-chains 251 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 8 optimal weight: 0.0980 chunk 181 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 246 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 58 optimal weight: 0.0020 chunk 67 optimal weight: 0.3980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 165 ASN B 120 GLN C 54 GLN C 337 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN D 330 ASN D 362 GLN E 219 HIS E 234 GLN E 287 GLN E 425 ASN E 594 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.117354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092564 restraints weight = 34900.932| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.54 r_work: 0.2994 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23208 Z= 0.118 Angle : 0.551 11.920 31757 Z= 0.292 Chirality : 0.042 0.376 3544 Planarity : 0.004 0.044 3898 Dihedral : 14.609 178.164 3971 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.40 % Favored : 97.48 % Rotamer: Outliers : 2.25 % Allowed : 17.99 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2664 helix: 1.11 (0.18), residues: 846 sheet: -0.45 (0.24), residues: 479 loop : 0.35 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 424 TYR 0.011 0.001 TYR E 573 PHE 0.012 0.001 PHE D 134 TRP 0.022 0.001 TRP A 532 HIS 0.003 0.001 HIS D 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (23208) covalent geometry : angle 0.55064 / 0.29 (31757) hydrogen bonds : bond 0.03677 / 2.51 ( 947) hydrogen bonds : angle 5.04624 / 3.54 ( 2593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6256 (mmt) REVERT: A 145 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 200 GLU cc_start: 0.8902 (tt0) cc_final: 0.8616 (tt0) REVERT: A 304 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 405 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: A 432 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8727 (mppt) REVERT: A 467 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8216 (mmtt) REVERT: A 469 THR cc_start: 0.8859 (m) cc_final: 0.8491 (p) REVERT: A 501 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7963 (tttt) REVERT: A 712 ASN cc_start: 0.8298 (m110) cc_final: 0.7963 (t0) REVERT: B 66 ASN cc_start: 0.8044 (m-40) cc_final: 0.7694 (m-40) REVERT: B 78 LEU cc_start: 0.8926 (mm) cc_final: 0.8596 (tp) REVERT: B 116 THR cc_start: 0.8932 (t) cc_final: 0.8726 (p) REVERT: B 168 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 23 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7372 (mt-10) REVERT: C 81 ASP cc_start: 0.6875 (p0) cc_final: 0.6287 (t0) REVERT: C 83 GLU cc_start: 0.8121 (tt0) cc_final: 0.7914 (tm-30) REVERT: C 152 ARG cc_start: 0.7154 (ttm110) cc_final: 0.6945 (ttp80) REVERT: C 188 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: C 211 ARG cc_start: 0.7860 (tmm160) cc_final: 0.7463 (ttp80) REVERT: C 223 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6865 (tm-30) REVERT: C 309 ASP cc_start: 0.6970 (t0) cc_final: 0.5942 (m-30) REVERT: C 351 ASP cc_start: 0.7794 (p0) cc_final: 0.7172 (m-30) REVERT: C 374 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5513 (tt) REVERT: C 417 ASP cc_start: 0.7192 (t0) cc_final: 0.6868 (t0) REVERT: C 420 ARG cc_start: 0.5898 (mpt180) cc_final: 0.4562 (mtm180) REVERT: C 509 GLN cc_start: 0.7714 (mm110) cc_final: 0.6832 (pm20) REVERT: C 515 LYS cc_start: 0.8346 (mttt) cc_final: 0.8048 (mttp) REVERT: D 4 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7819 (tmtm) REVERT: D 252 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8309 (t) REVERT: D 338 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7703 (ptp) REVERT: D 383 VAL cc_start: 0.8578 (m) cc_final: 0.8352 (p) REVERT: D 471 ASN cc_start: 0.8060 (t0) cc_final: 0.7815 (p0) REVERT: D 480 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: E 136 CYS cc_start: 0.8803 (t) cc_final: 0.8462 (m) REVERT: E 189 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8621 (mttt) REVERT: E 304 ARG cc_start: 0.8061 (tpt90) cc_final: 0.7836 (tpp80) REVERT: E 314 GLN cc_start: 0.8511 (tt0) cc_final: 0.8163 (mt0) REVERT: E 330 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7876 (ptm160) REVERT: E 452 MET cc_start: 0.9118 (mtp) cc_final: 0.8707 (mtt) REVERT: E 468 GLU cc_start: 0.8295 (tp30) cc_final: 0.8015 (tp30) REVERT: E 630 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8553 (tp30) outliers start: 51 outliers final: 23 residues processed: 251 average time/residue: 0.6282 time to fit residues: 179.5764 Evaluate side-chains 235 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 779 GLN B 120 GLN C 54 GLN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN D 362 GLN E 287 GLN E 594 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089609 restraints weight = 34696.825| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.93 r_work: 0.3028 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23208 Z= 0.138 Angle : 0.560 11.701 31757 Z= 0.295 Chirality : 0.043 0.383 3544 Planarity : 0.004 0.061 3898 Dihedral : 14.547 178.170 3969 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 2.08 % Allowed : 18.44 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2664 helix: 1.12 (0.18), residues: 846 sheet: -0.39 (0.24), residues: 481 loop : 0.35 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 362 TYR 0.012 0.001 TYR E 573 PHE 0.013 0.001 PHE E 734 TRP 0.016 0.001 TRP A 532 HIS 0.003 0.001 HIS E 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (23208) covalent geometry : angle 0.55986 / 0.29 (31757) hydrogen bonds : bond 0.03718 / 2.54 ( 947) hydrogen bonds : angle 5.02595 / 3.52 ( 2593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 20 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.6321 (mmt) REVERT: A 145 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 200 GLU cc_start: 0.8804 (tt0) cc_final: 0.8585 (tt0) REVERT: A 304 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 405 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 432 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8731 (mppt) REVERT: A 501 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7969 (tttt) REVERT: A 712 ASN cc_start: 0.8214 (m110) cc_final: 0.7953 (t0) REVERT: B 26 ASP cc_start: 0.8381 (t70) cc_final: 0.8143 (t0) REVERT: B 66 ASN cc_start: 0.7994 (m-40) cc_final: 0.7671 (m-40) REVERT: B 78 LEU cc_start: 0.8940 (mm) cc_final: 0.8608 (tp) REVERT: B 116 THR cc_start: 0.8929 (t) cc_final: 0.8725 (p) REVERT: B 168 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7618 (mt-10) REVERT: C 23 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 81 ASP cc_start: 0.6827 (p0) cc_final: 0.6274 (t0) REVERT: C 152 ARG cc_start: 0.7152 (ttm110) cc_final: 0.6950 (ttp80) REVERT: C 188 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: C 211 ARG cc_start: 0.7876 (tmm160) cc_final: 0.7474 (ttp80) REVERT: C 223 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6957 (tm-30) REVERT: C 309 ASP cc_start: 0.6955 (t0) cc_final: 0.5969 (m-30) REVERT: C 351 ASP cc_start: 0.7766 (p0) cc_final: 0.7190 (m-30) REVERT: C 374 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5442 (tt) REVERT: C 417 ASP cc_start: 0.7196 (t0) cc_final: 0.6857 (t0) REVERT: C 420 ARG cc_start: 0.5955 (mpt180) cc_final: 0.4638 (mtm180) REVERT: C 509 GLN cc_start: 0.7723 (mm110) cc_final: 0.6859 (pm20) REVERT: C 515 LYS cc_start: 0.8381 (mttt) cc_final: 0.8083 (mttp) REVERT: D 4 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7782 (tmtm) REVERT: D 480 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: E 136 CYS cc_start: 0.8708 (t) cc_final: 0.8432 (m) REVERT: E 189 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8617 (mttt) REVERT: E 304 ARG cc_start: 0.8034 (tpt90) cc_final: 0.7806 (tpp80) REVERT: E 314 GLN cc_start: 0.8433 (tt0) cc_final: 0.8113 (mt0) REVERT: E 330 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7864 (ptm160) REVERT: E 452 MET cc_start: 0.9081 (mtp) cc_final: 0.8800 (mtt) REVERT: E 468 GLU cc_start: 0.8194 (tp30) cc_final: 0.7918 (tp30) outliers start: 47 outliers final: 28 residues processed: 236 average time/residue: 0.6096 time to fit residues: 163.2253 Evaluate side-chains 242 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 594 GLN Chi-restraints excluded: chain E residue 630 GLU Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 245 optimal weight: 0.0870 chunk 237 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 90 optimal weight: 0.4980 chunk 39 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN B 120 GLN B 121 GLN C 54 GLN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN D 362 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090468 restraints weight = 34760.529| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.88 r_work: 0.3045 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23208 Z= 0.113 Angle : 0.550 12.164 31757 Z= 0.291 Chirality : 0.042 0.376 3544 Planarity : 0.004 0.045 3898 Dihedral : 14.549 178.145 3969 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.33 % Rotamer: Outliers : 1.77 % Allowed : 18.52 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2664 helix: 1.20 (0.18), residues: 846 sheet: -0.38 (0.23), residues: 481 loop : 0.38 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 362 TYR 0.011 0.001 TYR E 573 PHE 0.013 0.001 PHE D 134 TRP 0.021 0.001 TRP A 532 HIS 0.003 0.001 HIS D 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (23208) covalent geometry : angle 0.55044 / 0.29 (31757) hydrogen bonds : bond 0.03621 / 2.48 ( 947) hydrogen bonds : angle 4.95200 / 3.47 ( 2593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7963.07 seconds wall clock time: 136 minutes 22.52 seconds (8182.52 seconds total)