Starting phenix.real_space_refine on Sat Jul 4 16:44:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khf_62338/07_2026/9khf_62338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khf_62338/07_2026/9khf_62338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9khf_62338/07_2026/9khf_62338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khf_62338/07_2026/9khf_62338.map" model { file = "/net/cci-nas-00/data/ceres_data/9khf_62338/07_2026/9khf_62338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khf_62338/07_2026/9khf_62338.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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 K 2 8.98 5 S 100 5.16 5 C 14014 2.51 5 N 3602 2.21 5 O 3892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21610 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5408 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 19, 'TRANS': 647} Chain: "B" Number of atoms: 5396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5396 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 19, 'TRANS': 646} Chain: "C" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5408 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 19, 'TRANS': 647} Chain: "D" Number of atoms: 5396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5396 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 19, 'TRANS': 646} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 5.51, per 1000 atoms: 0.25 Number of scatterers: 21610 At special positions: 0 Unit cell: (103.88, 104.94, 185.5, 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) K 2 19.00 S 100 16.00 O 3892 8.00 N 3602 7.00 C 14014 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: 2.00 Conformation dependent library (CDL) restraints added in 834.1 milliseconds 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5004 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 11 sheets defined 67.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 62 through 89 removed outlier: 3.605A pdb=" N ALA A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 97 through 116 removed outlier: 4.038A pdb=" N ASP A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 164 through 170 removed outlier: 4.015A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 177 through 191 removed outlier: 4.247A pdb=" N VAL A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.965A pdb=" N ILE A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 313 removed outlier: 3.575A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 368 through 378 removed outlier: 3.929A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 455 through 462 Processing helix chain 'A' and resid 482 through 492 removed outlier: 4.041A pdb=" N ILE A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 510 removed outlier: 4.529A pdb=" N THR A 498 " --> pdb=" O HIS A 494 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.981A pdb=" N ARG A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 585 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.557A pdb=" N ILE A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 617 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 639 Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.656A pdb=" N SER A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 676 through 680 removed outlier: 4.008A pdb=" N LEU A 680 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.830A pdb=" N GLU A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 724 removed outlier: 5.151A pdb=" N ALA A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Proline residue: B 84 - end of helix removed outlier: 3.660A pdb=" N PHE B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 118 removed outlier: 3.759A pdb=" N ASP B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.661A pdb=" N ILE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.665A pdb=" N VAL B 167 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.801A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 225 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.614A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 3.582A pdb=" N ARG B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.544A pdb=" N MET B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 removed outlier: 3.518A pdb=" N ARG B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 352 Processing helix chain 'B' and resid 352 through 362 removed outlier: 4.531A pdb=" N THR B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 358 " --> pdb=" O HIS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.643A pdb=" N LYS B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.592A pdb=" N PHE B 387 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 400 Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 492 through 510 Processing helix chain 'B' and resid 517 through 542 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 640 through 651 Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.957A pdb=" N VAL B 667 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.855A pdb=" N ALA B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 706 through 723 Processing helix chain 'C' and resid 62 through 89 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 97 through 116 removed outlier: 4.000A pdb=" N ASP C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 144 through 150 Processing helix chain 'C' and resid 164 through 170 removed outlier: 4.004A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 191 removed outlier: 4.241A pdb=" N VAL C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.971A pdb=" N ILE C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 3.502A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 313 removed outlier: 3.577A pdb=" N MET C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 336 through 353 Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 368 through 378 removed outlier: 4.332A pdb=" N ILE C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 378 " --> pdb=" O GLN C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 455 through 462 Processing helix chain 'C' and resid 482 through 490 Processing helix chain 'C' and resid 492 through 510 Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.854A pdb=" N ARG C 574 " --> pdb=" O LEU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 585 Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.580A pdb=" N ILE C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 617 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 639 Processing helix chain 'C' and resid 640 through 650 removed outlier: 3.675A pdb=" N SER C 650 " --> pdb=" O ARG C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 672 Processing helix chain 'C' and resid 676 through 680 removed outlier: 3.985A pdb=" N LEU C 680 " --> pdb=" O ALA C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 705 removed outlier: 3.823A pdb=" N GLU C 700 " --> pdb=" O SER C 696 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 724 removed outlier: 5.119A pdb=" N ALA C 719 " --> pdb=" O ASP C 715 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN C 720 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Proline residue: D 84 - end of helix removed outlier: 3.651A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 118 removed outlier: 3.751A pdb=" N ASP D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 161 removed outlier: 3.671A pdb=" N ILE D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.664A pdb=" N VAL D 167 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP D 172 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.761A pdb=" N LYS D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 225 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.565A pdb=" N GLU D 231 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 313 removed outlier: 3.777A pdb=" N ILE D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 333 removed outlier: 3.561A pdb=" N ARG D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 333 " --> pdb=" O PHE D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 351 Processing helix chain 'D' and resid 352 through 355 removed outlier: 3.598A pdb=" N TYR D 355 " --> pdb=" O ASP D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 352 through 355' Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 482 through 492 Processing helix chain 'D' and resid 492 through 510 Processing helix chain 'D' and resid 517 through 542 Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 586 Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 627 through 639 Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.535A pdb=" N LEU D 644 " --> pdb=" O ASP D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 672 removed outlier: 4.130A pdb=" N VAL D 667 " --> pdb=" O THR D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 683 removed outlier: 3.820A pdb=" N ALA D 683 " --> pdb=" O MET D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 723 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.592A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.602A pdb=" N PHE A 407 " --> pdb=" O CYS A 475 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 475 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.700A pdb=" N VAL A 412 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 471 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 446 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.751A pdb=" N TYR B 120 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 412 through 414 removed outlier: 5.880A pdb=" N VAL B 412 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL B 471 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 431 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 422 through 425 Processing sheet with id=AA7, first strand: chain 'C' and resid 403 through 407 removed outlier: 3.634A pdb=" N PHE C 407 " --> pdb=" O CYS C 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS C 475 " --> pdb=" O PHE C 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.866A pdb=" N VAL C 412 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 471 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 431 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 446 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.766A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 405 through 407 removed outlier: 3.862A pdb=" N PHE D 407 " --> pdb=" O CYS D 475 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS D 475 " --> pdb=" O PHE D 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 412 through 414 removed outlier: 6.148A pdb=" N VAL D 412 " --> pdb=" O VAL D 471 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL D 471 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 414 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 431 " --> pdb=" O LEU D 448 " (cutoff:3.500A) 1253 hydrogen bonds defined for protein. 3624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3492 1.32 - 1.44: 6120 1.44 - 1.57: 12335 1.57 - 1.70: 3 1.70 - 1.82: 156 Bond restraints: 22106 Sorted by residual: bond pdb=" C TYR B 355 " pdb=" O TYR B 355 " ideal model delta sigma weight residual 1.235 1.316 -0.081 1.26e-02 6.30e+03 4.13e+01 bond pdb=" CA LEU B 386 " pdb=" C LEU B 386 " ideal model delta sigma weight residual 1.522 1.603 -0.081 1.39e-02 5.18e+03 3.39e+01 bond pdb=" N PRO A 600 " pdb=" CD PRO A 600 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.18e+01 bond pdb=" CA ARG B 340 " pdb=" C ARG B 340 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.32e-02 5.74e+03 1.92e+01 bond pdb=" CB ILE D 343 " pdb=" CG2 ILE D 343 " ideal model delta sigma weight residual 1.521 1.380 0.141 3.30e-02 9.18e+02 1.82e+01 ... (remaining 22101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 29441 2.93 - 5.86: 363 5.86 - 8.79: 74 8.79 - 11.72: 21 11.72 - 14.66: 1 Bond angle restraints: 29900 Sorted by residual: angle pdb=" N PHE A 596 " pdb=" CA PHE A 596 " pdb=" C PHE A 596 " ideal model delta sigma weight residual 112.87 122.97 -10.10 1.20e+00 6.94e-01 7.09e+01 angle pdb=" N ARG B 340 " pdb=" CA ARG B 340 " pdb=" C ARG B 340 " ideal model delta sigma weight residual 111.11 101.60 9.51 1.20e+00 6.94e-01 6.28e+01 angle pdb=" N LEU A 709 " pdb=" CA LEU A 709 " pdb=" C LEU A 709 " ideal model delta sigma weight residual 111.11 120.21 -9.10 1.20e+00 6.94e-01 5.75e+01 angle pdb=" N ARG A 63 " pdb=" CA ARG A 63 " pdb=" C ARG A 63 " ideal model delta sigma weight residual 111.02 120.22 -9.20 1.22e+00 6.72e-01 5.68e+01 angle pdb=" N TRP A 64 " pdb=" CA TRP A 64 " pdb=" C TRP A 64 " ideal model delta sigma weight residual 112.23 121.54 -9.31 1.26e+00 6.30e-01 5.46e+01 ... (remaining 29895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 10938 17.75 - 35.49: 1632 35.49 - 53.24: 414 53.24 - 70.99: 91 70.99 - 88.73: 33 Dihedral angle restraints: 13108 sinusoidal: 5316 harmonic: 7792 Sorted by residual: dihedral pdb=" C PRO D 365 " pdb=" N PRO D 365 " pdb=" CA PRO D 365 " pdb=" CB PRO D 365 " ideal model delta harmonic sigma weight residual -120.70 -107.47 -13.23 0 2.50e+00 1.60e-01 2.80e+01 dihedral pdb=" C ARG A 63 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " pdb=" CB ARG A 63 " ideal model delta harmonic sigma weight residual -122.60 -134.80 12.20 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" CA GLU D 231 " pdb=" C GLU D 231 " pdb=" N GLY D 232 " pdb=" CA GLY D 232 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 13105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3151 0.094 - 0.189: 164 0.189 - 0.283: 18 0.283 - 0.377: 4 0.377 - 0.471: 1 Chirality restraints: 3338 Sorted by residual: chirality pdb=" CA ARG A 63 " pdb=" N ARG A 63 " pdb=" C ARG A 63 " pdb=" CB ARG A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CA LEU A 581 " pdb=" N LEU A 581 " pdb=" C LEU A 581 " pdb=" CB LEU A 581 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU C 581 " pdb=" N LEU C 581 " pdb=" C LEU C 581 " pdb=" CB LEU C 581 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 3335 not shown) Planarity restraints: 3768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 491 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE C 491 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE C 491 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR C 492 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 274 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C TYR A 274 " 0.051 2.00e-02 2.50e+03 pdb=" O TYR A 274 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 275 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 274 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C TYR C 274 " 0.049 2.00e-02 2.50e+03 pdb=" O TYR C 274 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY C 275 " -0.017 2.00e-02 2.50e+03 ... (remaining 3765 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.66: 452 2.66 - 3.28: 25337 3.28 - 3.90: 43808 3.90 - 4.52: 57502 4.52 - 5.14: 86689 Nonbonded interactions: 213788 Sorted by model distance: nonbonded pdb=" O THR B 438 " pdb=" OD1 ASP B 439 " model vdw 2.041 3.040 nonbonded pdb=" O ASP D 439 " pdb=" OD1 ASP D 439 " model vdw 2.097 3.040 nonbonded pdb=" O ASP C 352 " pdb=" OD1 ASP C 352 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR C 268 " pdb=" OH TYR D 274 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP C 421 " pdb=" ND1 HIS C 422 " model vdw 2.214 3.120 ... (remaining 213783 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 58 through 723) selection = chain 'B' selection = (chain 'C' and resid 58 through 723) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.004 0.141 22106 Z= 0.254 Angle : 0.853 14.656 29900 Z= 0.506 Chirality : 0.049 0.471 3338 Planarity : 0.005 0.071 3768 Dihedral : 18.167 88.732 8104 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.79 % Favored : 93.57 % Rotamer: Outliers : 1.61 % Allowed : 29.61 % Favored : 68.78 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2658 helix: 0.51 (0.13), residues: 1636 sheet: -1.78 (0.48), residues: 128 loop : -1.71 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 369 TYR 0.033 0.002 TYR B 351 PHE 0.034 0.002 PHE D 623 TRP 0.012 0.001 TRP D 255 HIS 0.012 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.25 (22106) covalent geometry : angle 0.85263 / 0.51 (29900) hydrogen bonds : bond 0.15632 / 10.25 ( 1253) hydrogen bonds : angle 5.82715 / 4.18 ( 3624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7147 (pp20) REVERT: A 514 LYS cc_start: 0.5256 (mptt) cc_final: 0.4856 (mttt) REVERT: A 679 MET cc_start: 0.4805 (mmp) cc_final: 0.3257 (ptm) REVERT: B 161 SER cc_start: 0.8412 (t) cc_final: 0.8062 (p) REVERT: B 327 ILE cc_start: 0.8832 (mm) cc_final: 0.8354 (mm) REVERT: B 350 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: B 400 ILE cc_start: 0.8807 (tt) cc_final: 0.8557 (tt) REVERT: B 424 TYR cc_start: 0.6723 (m-80) cc_final: 0.6474 (m-80) REVERT: B 652 MET cc_start: 0.1221 (tmm) cc_final: -0.0299 (mmm) REVERT: C 183 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7080 (pp20) REVERT: C 487 ASN cc_start: 0.8266 (t0) cc_final: 0.8040 (t0) REVERT: C 508 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 514 LYS cc_start: 0.5022 (mptt) cc_final: 0.4408 (mttt) REVERT: C 652 MET cc_start: 0.1165 (tpt) cc_final: 0.0591 (ppp) REVERT: C 679 MET cc_start: 0.4982 (mmp) cc_final: 0.3529 (ptm) REVERT: D 137 PHE cc_start: 0.7138 (m-80) cc_final: 0.6853 (m-10) REVERT: D 161 SER cc_start: 0.8425 (t) cc_final: 0.8053 (p) REVERT: D 372 ILE cc_start: 0.8698 (mt) cc_final: 0.8295 (tt) outliers start: 38 outliers final: 19 residues processed: 307 average time/residue: 0.1526 time to fit residues: 72.9465 Evaluate side-chains 222 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 560 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.0000 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 GLN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN B 718 ASN C 465 GLN ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.257709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.231804 restraints weight = 25933.974| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 1.62 r_work: 0.4178 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.4139 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work: 0.4006 rms_B_bonded: 4.94 restraints_weight: 0.1250 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22106 Z= 0.138 Angle : 0.629 9.976 29900 Z= 0.325 Chirality : 0.041 0.176 3338 Planarity : 0.005 0.060 3768 Dihedral : 5.865 58.119 2973 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.08 % Favored : 94.70 % Rotamer: Outliers : 3.65 % Allowed : 27.53 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2658 helix: 0.72 (0.12), residues: 1684 sheet: -1.67 (0.46), residues: 122 loop : -1.45 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 369 TYR 0.029 0.001 TYR B 355 PHE 0.035 0.002 PHE A 582 TRP 0.011 0.001 TRP D 255 HIS 0.008 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (22106) covalent geometry : angle 0.62917 / 0.32 (29900) hydrogen bonds : bond 0.05248 / 3.40 ( 1253) hydrogen bonds : angle 4.55711 / 3.30 ( 3624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 237 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 282 LEU cc_start: 0.8612 (tp) cc_final: 0.7723 (mt) REVERT: A 514 LYS cc_start: 0.5261 (mptt) cc_final: 0.4793 (mttt) REVERT: A 679 MET cc_start: 0.4261 (mmp) cc_final: 0.3197 (ptm) REVERT: B 175 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8615 (tp) REVERT: B 252 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8583 (mt) REVERT: B 400 ILE cc_start: 0.8455 (tt) cc_final: 0.8197 (tt) REVERT: B 652 MET cc_start: 0.0686 (tmm) cc_final: -0.0250 (mmm) REVERT: B 700 GLU cc_start: 0.1697 (OUTLIER) cc_final: 0.1271 (mt-10) REVERT: C 282 LEU cc_start: 0.8589 (tp) cc_final: 0.7631 (mt) REVERT: C 408 LEU cc_start: 0.8126 (mt) cc_final: 0.7906 (mp) REVERT: C 487 ASN cc_start: 0.7189 (t0) cc_final: 0.6977 (t0) REVERT: C 508 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: C 514 LYS cc_start: 0.5102 (mptt) cc_final: 0.4396 (mttt) REVERT: C 652 MET cc_start: 0.1160 (tpt) cc_final: 0.0565 (ppp) REVERT: C 679 MET cc_start: 0.4571 (mmp) cc_final: 0.3474 (ptm) REVERT: D 137 PHE cc_start: 0.7740 (m-80) cc_final: 0.7505 (m-10) REVERT: D 175 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8545 (tp) REVERT: D 323 MET cc_start: 0.8446 (mmm) cc_final: 0.8169 (mmm) REVERT: D 346 HIS cc_start: 0.5274 (t70) cc_final: 0.5035 (t70) outliers start: 86 outliers final: 33 residues processed: 310 average time/residue: 0.1466 time to fit residues: 73.1815 Evaluate side-chains 238 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 249 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS B 510 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.255072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.228181 restraints weight = 25688.000| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.42 r_work: 0.4186 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work: 0.4032 rms_B_bonded: 4.16 restraints_weight: 0.1250 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22106 Z= 0.165 Angle : 0.631 11.589 29900 Z= 0.322 Chirality : 0.042 0.184 3338 Planarity : 0.004 0.061 3768 Dihedral : 5.281 49.189 2951 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.34 % Favored : 94.43 % Rotamer: Outliers : 3.82 % Allowed : 27.95 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2658 helix: 0.82 (0.13), residues: 1668 sheet: -1.04 (0.50), residues: 106 loop : -1.41 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 127 TYR 0.023 0.002 TYR C 130 PHE 0.027 0.002 PHE C 582 TRP 0.011 0.001 TRP D 255 HIS 0.011 0.001 HIS D 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (22106) covalent geometry : angle 0.63095 / 0.32 (29900) hydrogen bonds : bond 0.05143 / 3.32 ( 1253) hydrogen bonds : angle 4.44988 / 3.23 ( 3624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 209 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 234 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 282 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8162 (mt) REVERT: A 514 LYS cc_start: 0.5346 (mptt) cc_final: 0.4852 (mttt) REVERT: B 146 MET cc_start: 0.7836 (mmp) cc_final: 0.7552 (mmm) REVERT: B 175 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 400 ILE cc_start: 0.8374 (tt) cc_final: 0.8123 (tt) REVERT: B 652 MET cc_start: 0.0653 (tmm) cc_final: -0.0303 (mmm) REVERT: B 700 GLU cc_start: 0.1492 (OUTLIER) cc_final: 0.1291 (mt-10) REVERT: C 234 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.9020 (p) REVERT: C 282 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8119 (mt) REVERT: C 360 MET cc_start: 0.8143 (tmm) cc_final: 0.7881 (tmm) REVERT: C 408 LEU cc_start: 0.8229 (mt) cc_final: 0.7969 (mp) REVERT: C 487 ASN cc_start: 0.7120 (t0) cc_final: 0.6865 (t0) REVERT: C 504 MET cc_start: 0.7031 (ppp) cc_final: 0.6654 (ppp) REVERT: C 508 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6288 (mt-10) REVERT: C 514 LYS cc_start: 0.5124 (mptt) cc_final: 0.4601 (mttp) REVERT: C 652 MET cc_start: 0.1017 (tpt) cc_final: 0.0573 (ppp) REVERT: C 679 MET cc_start: 0.4497 (mmp) cc_final: 0.3580 (ptm) REVERT: D 175 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.7897 (mp) REVERT: D 323 MET cc_start: 0.8391 (mmm) cc_final: 0.8127 (mmm) REVERT: D 339 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5156 (mt) REVERT: D 372 ILE cc_start: 0.8395 (mt) cc_final: 0.8193 (tt) outliers start: 90 outliers final: 48 residues processed: 284 average time/residue: 0.1480 time to fit residues: 68.0410 Evaluate side-chains 253 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 566 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 93 optimal weight: 0.0170 chunk 49 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 121 optimal weight: 40.0000 chunk 196 optimal weight: 6.9990 chunk 263 optimal weight: 30.0000 chunk 161 optimal weight: 0.5980 chunk 237 optimal weight: 10.0000 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 510 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.257136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.230735 restraints weight = 25985.783| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 1.63 r_work: 0.4215 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4167 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22106 Z= 0.122 Angle : 0.591 12.946 29900 Z= 0.297 Chirality : 0.039 0.163 3338 Planarity : 0.004 0.057 3768 Dihedral : 5.084 49.852 2945 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.12 % Favored : 94.66 % Rotamer: Outliers : 3.74 % Allowed : 27.70 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2658 helix: 1.01 (0.13), residues: 1678 sheet: -0.58 (0.53), residues: 96 loop : -1.33 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 470 TYR 0.024 0.001 TYR C 130 PHE 0.026 0.001 PHE C 582 TRP 0.009 0.001 TRP D 235 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (22106) covalent geometry : angle 0.59115 / 0.30 (29900) hydrogen bonds : bond 0.04439 / 2.86 ( 1253) hydrogen bonds : angle 4.20652 / 3.06 ( 3624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 210 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 234 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8960 (p) REVERT: A 282 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 514 LYS cc_start: 0.5199 (mptt) cc_final: 0.4757 (mttt) REVERT: A 598 HIS cc_start: 0.4510 (OUTLIER) cc_final: 0.4106 (m-70) REVERT: B 146 MET cc_start: 0.7587 (mmp) cc_final: 0.7371 (mmm) REVERT: B 175 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 400 ILE cc_start: 0.8234 (tt) cc_final: 0.7972 (tt) REVERT: B 652 MET cc_start: 0.0704 (tmm) cc_final: -0.0141 (mmm) REVERT: B 700 GLU cc_start: 0.1620 (OUTLIER) cc_final: 0.0810 (mt-10) REVERT: C 234 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8976 (p) REVERT: C 282 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 487 ASN cc_start: 0.6891 (t0) cc_final: 0.6634 (t0) REVERT: C 508 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6299 (mt-10) REVERT: C 514 LYS cc_start: 0.4893 (mptt) cc_final: 0.4537 (mttt) REVERT: C 652 MET cc_start: 0.0946 (tpt) cc_final: 0.0642 (ppp) REVERT: C 679 MET cc_start: 0.4480 (mmp) cc_final: 0.3614 (ptm) REVERT: D 175 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.7571 (mp) REVERT: D 339 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.5016 (mt) outliers start: 88 outliers final: 50 residues processed: 278 average time/residue: 0.1468 time to fit residues: 65.8629 Evaluate side-chains 253 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 460 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 220 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 207 optimal weight: 0.0030 chunk 211 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 218 optimal weight: 0.5980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 GLN A 502 ASN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.255184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.230391 restraints weight = 25680.572| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 1.52 r_work: 0.4199 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work: 0.4062 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22106 Z= 0.152 Angle : 0.597 10.451 29900 Z= 0.304 Chirality : 0.040 0.173 3338 Planarity : 0.004 0.055 3768 Dihedral : 4.952 49.121 2943 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.43 % Rotamer: Outliers : 4.55 % Allowed : 27.70 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2658 helix: 0.99 (0.13), residues: 1682 sheet: -1.07 (0.45), residues: 126 loop : -1.25 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 470 TYR 0.015 0.001 TYR A 380 PHE 0.025 0.001 PHE C 582 TRP 0.011 0.001 TRP D 235 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (22106) covalent geometry : angle 0.59732 / 0.30 (29900) hydrogen bonds : bond 0.04706 / 3.04 ( 1253) hydrogen bonds : angle 4.19237 / 3.06 ( 3624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 207 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8816 (mp) REVERT: A 234 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8988 (p) REVERT: A 282 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 514 LYS cc_start: 0.5338 (mptt) cc_final: 0.4851 (mttt) REVERT: A 598 HIS cc_start: 0.4646 (OUTLIER) cc_final: 0.4240 (m-70) REVERT: B 175 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 339 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.4991 (mt) REVERT: B 400 ILE cc_start: 0.8298 (tt) cc_final: 0.8061 (tt) REVERT: B 652 MET cc_start: 0.0907 (tmm) cc_final: 0.0066 (mmm) REVERT: B 700 GLU cc_start: 0.1654 (OUTLIER) cc_final: 0.0849 (mt-10) REVERT: C 234 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9001 (p) REVERT: C 282 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.7875 (mp) REVERT: C 487 ASN cc_start: 0.6995 (t0) cc_final: 0.6708 (t0) REVERT: C 508 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6378 (mt-10) REVERT: C 514 LYS cc_start: 0.5127 (mptt) cc_final: 0.4694 (mttt) REVERT: C 652 MET cc_start: 0.0985 (tpt) cc_final: 0.0653 (ppp) REVERT: C 679 MET cc_start: 0.4444 (mmp) cc_final: 0.3586 (ptm) REVERT: D 175 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.7960 (mp) REVERT: D 339 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5066 (mt) outliers start: 107 outliers final: 59 residues processed: 296 average time/residue: 0.1458 time to fit residues: 69.6446 Evaluate side-chains 255 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 693 TRP Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 460 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 200 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 502 ASN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS B 483 GLN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.252523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.225900 restraints weight = 25559.844| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 1.53 r_work: 0.4160 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22106 Z= 0.223 Angle : 0.655 13.082 29900 Z= 0.334 Chirality : 0.043 0.207 3338 Planarity : 0.004 0.054 3768 Dihedral : 5.037 50.756 2943 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.79 % Favored : 94.02 % Rotamer: Outliers : 4.55 % Allowed : 27.95 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.11 (0.16), residues: 2658 helix: 0.88 (0.12), residues: 1682 sheet: -0.93 (0.45), residues: 116 loop : -1.32 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 127 TYR 0.015 0.002 TYR A 220 PHE 0.024 0.002 PHE A 582 TRP 0.013 0.002 TRP D 235 HIS 0.018 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 (22106) covalent geometry : angle 0.65539 / 0.33 (29900) hydrogen bonds : bond 0.05313 / 3.44 ( 1253) hydrogen bonds : angle 4.30261 / 3.14 ( 3624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 199 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 282 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8539 (mt) REVERT: A 514 LYS cc_start: 0.5256 (mptt) cc_final: 0.4780 (mttt) REVERT: A 598 HIS cc_start: 0.4470 (OUTLIER) cc_final: 0.4072 (m-70) REVERT: B 339 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.4851 (mp) REVERT: B 375 LEU cc_start: 0.8333 (tt) cc_final: 0.8122 (tp) REVERT: B 400 ILE cc_start: 0.8273 (tt) cc_final: 0.8025 (tt) REVERT: B 652 MET cc_start: 0.0874 (tmm) cc_final: 0.0289 (mmm) REVERT: B 676 MET cc_start: 0.1643 (ppp) cc_final: 0.0337 (ttt) REVERT: C 130 TYR cc_start: 0.6708 (m-10) cc_final: 0.6372 (m-80) REVERT: C 175 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8686 (mp) REVERT: C 234 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (p) REVERT: C 282 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8516 (mt) REVERT: C 487 ASN cc_start: 0.6966 (t0) cc_final: 0.6672 (t0) REVERT: C 508 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: C 514 LYS cc_start: 0.5104 (mptt) cc_final: 0.4728 (mttt) REVERT: C 652 MET cc_start: 0.0937 (tpt) cc_final: 0.0584 (ppp) REVERT: C 679 MET cc_start: 0.4400 (mmp) cc_final: 0.3681 (ptm) REVERT: D 339 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.4878 (mt) outliers start: 107 outliers final: 79 residues processed: 289 average time/residue: 0.1417 time to fit residues: 66.5335 Evaluate side-chains 274 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 186 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 476 HIS Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 TRP Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 254 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.253538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.227528 restraints weight = 25579.704| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 1.54 r_work: 0.4193 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work: 0.4059 rms_B_bonded: 4.14 restraints_weight: 0.1250 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22106 Z= 0.178 Angle : 0.624 11.672 29900 Z= 0.318 Chirality : 0.041 0.197 3338 Planarity : 0.004 0.054 3768 Dihedral : 5.020 51.401 2943 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.57 % Favored : 94.28 % Rotamer: Outliers : 4.29 % Allowed : 28.21 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.16), residues: 2658 helix: 0.93 (0.13), residues: 1676 sheet: -0.68 (0.48), residues: 106 loop : -1.30 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 127 TYR 0.018 0.002 TYR A 139 PHE 0.024 0.002 PHE C 582 TRP 0.011 0.001 TRP D 235 HIS 0.019 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (22106) covalent geometry : angle 0.62357 / 0.32 (29900) hydrogen bonds : bond 0.05025 / 3.24 ( 1253) hydrogen bonds : angle 4.23592 / 3.09 ( 3624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 198 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 234 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9037 (p) REVERT: A 282 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 514 LYS cc_start: 0.5357 (mptt) cc_final: 0.4855 (mttt) REVERT: A 598 HIS cc_start: 0.4610 (OUTLIER) cc_final: 0.4235 (m-70) REVERT: B 339 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4843 (mt) REVERT: B 400 ILE cc_start: 0.8296 (tt) cc_final: 0.8044 (tt) REVERT: B 652 MET cc_start: 0.0870 (tmm) cc_final: 0.0363 (mmm) REVERT: C 130 TYR cc_start: 0.6714 (m-10) cc_final: 0.6455 (m-80) REVERT: C 175 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8776 (mp) REVERT: C 234 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9048 (p) REVERT: C 282 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8075 (mt) REVERT: C 487 ASN cc_start: 0.6939 (t0) cc_final: 0.6639 (t0) REVERT: C 508 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6435 (mt-10) REVERT: C 514 LYS cc_start: 0.5195 (mptt) cc_final: 0.4795 (mttt) REVERT: C 652 MET cc_start: 0.1015 (tpt) cc_final: 0.0667 (ppp) REVERT: C 679 MET cc_start: 0.4501 (mmp) cc_final: 0.3795 (ptm) REVERT: D 360 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6339 (ppp) REVERT: D 406 TYR cc_start: 0.7445 (m-10) cc_final: 0.7237 (m-10) outliers start: 101 outliers final: 78 residues processed: 284 average time/residue: 0.1397 time to fit residues: 65.0937 Evaluate side-chains 275 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 187 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 693 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 TRP Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 116 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 HIS A 451 HIS ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS D 483 GLN ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.248289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.225322 restraints weight = 25526.076| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 1.15 r_work: 0.4189 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.4069 rms_B_bonded: 3.28 restraints_weight: 0.1250 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.111 22106 Z= 0.389 Angle : 0.790 11.250 29900 Z= 0.410 Chirality : 0.050 0.210 3338 Planarity : 0.005 0.057 3768 Dihedral : 5.402 53.387 2943 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.09 % Favored : 93.75 % Rotamer: Outliers : 4.38 % Allowed : 28.72 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2658 helix: 0.50 (0.12), residues: 1684 sheet: -0.69 (0.50), residues: 108 loop : -1.57 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 127 TYR 0.025 0.003 TYR C 139 PHE 0.030 0.003 PHE D 108 TRP 0.016 0.003 TRP D 235 HIS 0.010 0.002 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.39 (22106) covalent geometry : angle 0.79039 / 0.41 (29900) hydrogen bonds : bond 0.06707 / 4.33 ( 1253) hydrogen bonds : angle 4.63831 / 3.37 ( 3624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 194 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8816 (mp) REVERT: A 514 LYS cc_start: 0.5290 (mptt) cc_final: 0.4970 (mttt) REVERT: B 400 ILE cc_start: 0.8178 (tt) cc_final: 0.7939 (tt) REVERT: B 652 MET cc_start: 0.0762 (tmm) cc_final: 0.0545 (mmm) REVERT: B 676 MET cc_start: 0.2659 (ppp) cc_final: 0.1336 (ttt) REVERT: C 175 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 487 ASN cc_start: 0.6931 (t0) cc_final: 0.6645 (t0) REVERT: C 508 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6500 (mt-10) REVERT: C 514 LYS cc_start: 0.5141 (mptt) cc_final: 0.4679 (mttt) REVERT: C 652 MET cc_start: 0.1059 (tpt) cc_final: 0.0619 (ppp) REVERT: C 679 MET cc_start: 0.4421 (mmp) cc_final: 0.3873 (ptm) REVERT: D 91 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7829 (mtt90) REVERT: D 266 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8696 (tt) outliers start: 103 outliers final: 75 residues processed: 281 average time/residue: 0.1384 time to fit residues: 64.3130 Evaluate side-chains 267 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 187 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 TRP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 37 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 HIS ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS D 666 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.252654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.223485 restraints weight = 25569.024| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 1.45 r_work: 0.4257 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22106 Z= 0.168 Angle : 0.646 10.705 29900 Z= 0.328 Chirality : 0.042 0.198 3338 Planarity : 0.004 0.056 3768 Dihedral : 5.223 56.841 2943 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.27 % Favored : 94.58 % Rotamer: Outliers : 3.23 % Allowed : 29.82 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2658 helix: 0.77 (0.12), residues: 1684 sheet: -0.79 (0.48), residues: 118 loop : -1.37 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 127 TYR 0.023 0.001 TYR C 380 PHE 0.029 0.002 PHE A 454 TRP 0.040 0.002 TRP A 693 HIS 0.018 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (22106) covalent geometry : angle 0.64626 / 0.33 (29900) hydrogen bonds : bond 0.05186 / 3.35 ( 1253) hydrogen bonds : angle 4.29961 / 3.13 ( 3624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 194 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8686 (mp) REVERT: A 514 LYS cc_start: 0.5142 (mptt) cc_final: 0.4890 (mttt) REVERT: B 175 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 400 ILE cc_start: 0.8083 (tt) cc_final: 0.7858 (tt) REVERT: B 676 MET cc_start: 0.2681 (ppp) cc_final: 0.1282 (ttt) REVERT: B 700 GLU cc_start: 0.1921 (OUTLIER) cc_final: 0.1290 (mt-10) REVERT: C 175 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8659 (mp) REVERT: C 487 ASN cc_start: 0.6563 (t0) cc_final: 0.6300 (t0) REVERT: C 508 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6210 (mt-10) REVERT: C 514 LYS cc_start: 0.5109 (mptt) cc_final: 0.4703 (mttt) REVERT: C 652 MET cc_start: 0.0913 (tpt) cc_final: 0.0633 (ppp) REVERT: C 679 MET cc_start: 0.4088 (mmp) cc_final: 0.3606 (ptm) REVERT: C 708 LYS cc_start: 0.5261 (OUTLIER) cc_final: 0.5058 (tptp) REVERT: D 121 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6927 (ttm170) REVERT: D 179 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7875 (ttm110) REVERT: D 339 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.4858 (mt) outliers start: 76 outliers final: 63 residues processed: 261 average time/residue: 0.1443 time to fit residues: 61.0602 Evaluate side-chains 260 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 TRP Chi-restraints excluded: chain C residue 708 LYS Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 460 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 56 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 216 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.255062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.227056 restraints weight = 25830.262| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 1.65 r_work: 0.4269 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4238 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22106 Z= 0.128 Angle : 0.617 11.933 29900 Z= 0.309 Chirality : 0.040 0.199 3338 Planarity : 0.004 0.054 3768 Dihedral : 4.967 59.805 2940 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.24 % Rotamer: Outliers : 2.68 % Allowed : 30.29 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 2658 helix: 1.00 (0.13), residues: 1682 sheet: -0.76 (0.48), residues: 118 loop : -1.28 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 127 TYR 0.014 0.001 TYR A 139 PHE 0.030 0.001 PHE A 454 TRP 0.022 0.001 TRP A 693 HIS 0.006 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (22106) covalent geometry : angle 0.61679 / 0.31 (29900) hydrogen bonds : bond 0.04446 / 2.87 ( 1253) hydrogen bonds : angle 4.13717 / 3.01 ( 3624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 514 LYS cc_start: 0.5127 (mptt) cc_final: 0.4905 (mttt) REVERT: B 175 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.7656 (mp) REVERT: B 339 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4626 (mp) REVERT: B 400 ILE cc_start: 0.8094 (tt) cc_final: 0.7860 (tt) REVERT: B 676 MET cc_start: 0.2865 (ppp) cc_final: 0.1198 (ttt) REVERT: B 700 GLU cc_start: 0.1911 (OUTLIER) cc_final: 0.1295 (mt-10) REVERT: C 127 ARG cc_start: 0.6359 (mmm160) cc_final: 0.5914 (mmm160) REVERT: C 175 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8670 (mp) REVERT: C 487 ASN cc_start: 0.6515 (t0) cc_final: 0.6237 (t0) REVERT: C 508 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6228 (mt-10) REVERT: C 514 LYS cc_start: 0.5112 (mptt) cc_final: 0.4697 (mttt) REVERT: C 679 MET cc_start: 0.3944 (mmp) cc_final: 0.3491 (ptm) REVERT: D 121 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6900 (ttm170) REVERT: D 175 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.7813 (mp) REVERT: D 179 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7796 (ttm110) REVERT: D 339 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.4808 (mt) REVERT: D 374 GLN cc_start: 0.7553 (pp30) cc_final: 0.7334 (pp30) outliers start: 63 outliers final: 44 residues processed: 257 average time/residue: 0.1473 time to fit residues: 61.0279 Evaluate side-chains 245 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 700 GLU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 TRP Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 460 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 105 optimal weight: 3.9990 chunk 142 optimal weight: 0.1980 chunk 181 optimal weight: 8.9990 chunk 84 optimal weight: 0.0170 chunk 187 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.0000 chunk 203 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 32 optimal weight: 0.0060 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 487 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.257546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.230142 restraints weight = 26002.653| |-----------------------------------------------------------------------------| r_work (start): 0.4494 rms_B_bonded: 1.69 r_work: 0.4189 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.4149 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22106 Z= 0.119 Angle : 0.625 12.233 29900 Z= 0.309 Chirality : 0.039 0.202 3338 Planarity : 0.004 0.056 3768 Dihedral : 4.874 58.859 2940 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.27 % Favored : 94.58 % Rotamer: Outliers : 2.46 % Allowed : 30.76 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2658 helix: 1.22 (0.13), residues: 1672 sheet: -0.73 (0.47), residues: 118 loop : -1.17 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 470 TYR 0.013 0.001 TYR B 220 PHE 0.029 0.001 PHE A 454 TRP 0.028 0.001 TRP A 693 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (22106) covalent geometry : angle 0.62544 / 0.31 (29900) hydrogen bonds : bond 0.04032 / 2.61 ( 1253) hydrogen bonds : angle 4.00624 / 2.91 ( 3624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.98 seconds wall clock time: 91 minutes 48.66 seconds (5508.66 seconds total)