Starting phenix.real_space_refine on Sun Aug 9 01:17:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gbv_51222/08_2026/9gbv_51222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gbv_51222/08_2026/9gbv_51222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gbv_51222/08_2026/9gbv_51222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gbv_51222/08_2026/9gbv_51222.map" model { file = "/net/cci-nas-00/data/ceres_data/9gbv_51222/08_2026/9gbv_51222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gbv_51222/08_2026/9gbv_51222.cif" } resolution = 2.32 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= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 318 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 18998 2.51 5 N 5706 2.21 5 O 6770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31890 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6519 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 28, 'TRANS': 807} Chain: "C" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6519 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 28, 'TRANS': 807} Chain: "B" Number of atoms: 6170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 782, 6161 Classifications: {'peptide': 782} Link IDs: {'PTRANS': 28, 'TRANS': 753} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 782, 6161 Classifications: {'peptide': 782} Link IDs: {'PTRANS': 28, 'TRANS': 753} Chain breaks: 1 bond proxies already assigned to first conformer: 6256 Chain: "D" Number of atoms: 6161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6161 Classifications: {'peptide': 782} Link IDs: {'PTRANS': 28, 'TRANS': 753} Chain breaks: 1 Chain: "E" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3239 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "F" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3280 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN B 542 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 542 " occ=0.50 Time building chain proxies: 7.41, per 1000 atoms: 0.23 Number of scatterers: 31890 At special positions: 0 Unit cell: (152.22, 203.82, 209.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 318 15.00 Mg 2 11.99 O 6770 8.00 N 5706 7.00 C 18998 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5986 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 41 sheets defined 39.9% alpha, 18.3% beta 150 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.592A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 346 through 387 removed outlier: 3.518A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.675A pdb=" N HIS A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.689A pdb=" N VAL A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.517A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 420 through 426' Processing helix chain 'A' and resid 428 through 432 removed outlier: 4.012A pdb=" N ALA A 432 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.512A pdb=" N ASP A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.850A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 4.006A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.700A pdb=" N ASN A 621 " --> pdb=" O PRO A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 664 Processing helix chain 'A' and resid 709 through 711 No H-bonds generated for 'chain 'A' and resid 709 through 711' Processing helix chain 'A' and resid 757 through 761 removed outlier: 3.833A pdb=" N GLU A 760 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 761 " --> pdb=" O VAL A 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 757 through 761' Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 81 through 92 removed outlier: 4.086A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 removed outlier: 3.982A pdb=" N ALA C 136 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 201 Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.520A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 387 removed outlier: 3.617A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 402 through 411 removed outlier: 3.777A pdb=" N VAL C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 426 removed outlier: 3.580A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 removed outlier: 3.573A pdb=" N ASP C 460 " --> pdb=" O GLN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.761A pdb=" N LEU C 466 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 493 removed outlier: 3.601A pdb=" N HIS C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 514 removed outlier: 3.640A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'C' and resid 661 through 664 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.932A pdb=" N ARG B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.963A pdb=" N VAL B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.536A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 279 through 300 Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.507A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 364 removed outlier: 4.174A pdb=" N SER B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.614A pdb=" N LYS B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.584A pdb=" N SER B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 434 removed outlier: 3.669A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.708A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 562 removed outlier: 3.597A pdb=" N LEU B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 562 " --> pdb=" O SER B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 597 removed outlier: 3.508A pdb=" N ASN B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.521A pdb=" N LYS B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.562A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 698 removed outlier: 3.731A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 removed outlier: 3.541A pdb=" N ARG B 731 " --> pdb=" O VAL B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 785 through 797 Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.920A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 26 Processing helix chain 'D' and resid 34 through 51 removed outlier: 4.281A pdb=" N VAL D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 184 through 198 removed outlier: 3.590A pdb=" N ARG D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 279 through 300 removed outlier: 3.964A pdb=" N ALA D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 311 through 316 removed outlier: 3.549A pdb=" N ALA D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 364 removed outlier: 3.691A pdb=" N GLN D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.778A pdb=" N ALA D 368 " --> pdb=" O ASN D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 removed outlier: 3.632A pdb=" N SER D 418 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 434 Processing helix chain 'D' and resid 457 through 464 Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 484 through 488 removed outlier: 4.078A pdb=" N LEU D 488 " --> pdb=" O PRO D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 518 removed outlier: 3.527A pdb=" N SER D 504 " --> pdb=" O ASP D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.807A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 576 through 596 Processing helix chain 'D' and resid 602 through 609 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 625 through 640 Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.579A pdb=" N ILE D 682 " --> pdb=" O ASP D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 698 removed outlier: 3.690A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 731 removed outlier: 3.605A pdb=" N ARG D 731 " --> pdb=" O VAL D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 745 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 785 through 796 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 6.347A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 removed outlier: 4.193A pdb=" N TYR A 241 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.800A pdb=" N ARG A 245 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 292 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU A 306 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA8, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 549 through 553 removed outlier: 3.759A pdb=" N LYS A 550 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 543 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 580 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 603 removed outlier: 3.556A pdb=" N ALA A 633 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 682 through 688 removed outlier: 4.195A pdb=" N THR A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 732 through 736 removed outlier: 3.887A pdb=" N SER A 734 " --> pdb=" O PHE A 697 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 697 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 755 through 756 removed outlier: 3.604A pdb=" N ALA A 743 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 785 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 752 through 753 Processing sheet with id=AB6, first strand: chain 'A' and resid 802 through 808 removed outlier: 6.018A pdb=" N THR A 803 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR A 799 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 798 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 8 through 12 removed outlier: 5.843A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE D 495 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB9, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AC1, first strand: chain 'C' and resid 171 through 174 removed outlier: 3.535A pdb=" N GLY C 173 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 333 removed outlier: 4.269A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.776A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 307 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL C 304 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU C 292 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU C 306 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AC5, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AC6, first strand: chain 'C' and resid 578 through 585 removed outlier: 3.956A pdb=" N ARG C 580 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 543 " --> pdb=" O ARG C 580 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER C 544 " --> pdb=" O TYR C 548 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 617 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 599 through 603 removed outlier: 3.778A pdb=" N ALA C 633 " --> pdb=" O PHE C 593 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 682 through 688 removed outlier: 3.586A pdb=" N GLY C 684 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR C 654 " --> pdb=" O THR C 650 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.861A pdb=" N SER C 734 " --> pdb=" O PHE C 697 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 697 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 694 " --> pdb=" O PHE C 706 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 783 through 788 removed outlier: 3.896A pdb=" N GLY C 785 " --> pdb=" O ALA C 747 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 746 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C 754 " --> pdb=" O THR C 746 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 805 through 808 removed outlier: 3.825A pdb=" N ILE C 798 " --> pdb=" O GLY C 835 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 149 through 150 removed outlier: 6.625A pdb=" N ILE B 140 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 142 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 155 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.763A pdb=" N LYS B 129 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 169 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 69 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 212 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 241 through 247 removed outlier: 3.528A pdb=" N PHE B 241 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 251 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B 265 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL B 323 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 267 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL B 325 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 269 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AD7, first strand: chain 'B' and resid 564 through 567 removed outlier: 3.682A pdb=" N PHE B 706 " --> pdb=" O HIS B 567 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 705 " --> pdb=" O VAL B 716 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 712 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 646 through 653 Processing sheet with id=AD9, first strand: chain 'D' and resid 149 through 150 removed outlier: 4.083A pdb=" N GLY D 158 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG D 142 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL D 156 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.839A pdb=" N LYS D 129 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN D 135 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR D 165 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 69 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 59 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG D 206 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 61 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 212 " --> pdb=" O ASP D 207 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 241 through 246 removed outlier: 6.761A pdb=" N ASN D 265 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL D 323 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR D 267 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL D 325 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE D 269 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N CYS D 268 " --> pdb=" O GLN D 275 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AE4, first strand: chain 'D' and resid 564 through 567 removed outlier: 3.790A pdb=" N ARG D 712 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 646 through 653 removed outlier: 3.503A pdb=" N GLN D 646 " --> pdb=" O ARG D 667 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 9.92 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8620 1.33 - 1.45: 6574 1.45 - 1.57: 17068 1.57 - 1.69: 634 1.69 - 1.81: 174 Bond restraints: 33070 Sorted by residual: bond pdb=" C3' DC F 31 " pdb=" C2' DC F 31 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC E -31 " pdb=" C2' DC E -31 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA E -18 " pdb=" C2' DA E -18 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA F -27 " pdb=" C2' DA F -27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA E 29 " pdb=" C2' DA E 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 ... (remaining 33065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 44230 1.34 - 2.68: 1705 2.68 - 4.02: 131 4.02 - 5.36: 9 5.36 - 6.71: 5 Bond angle restraints: 46080 Sorted by residual: angle pdb=" O4' DG F 67 " pdb=" C4' DG F 67 " pdb=" C3' DG F 67 " ideal model delta sigma weight residual 106.00 102.73 3.27 6.00e-01 2.78e+00 2.98e+01 angle pdb=" O4' DG F 21 " pdb=" C4' DG F 21 " pdb=" C3' DG F 21 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.75e+01 angle pdb=" O4' DG E 27 " pdb=" C4' DG E 27 " pdb=" C3' DG E 27 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" O4' DA E 19 " pdb=" C4' DA E 19 " pdb=" C3' DA E 19 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" O4' DT E 72 " pdb=" C4' DT E 72 " pdb=" C3' DT E 72 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.38e+01 ... (remaining 46075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 17975 35.35 - 70.71: 1339 70.71 - 106.06: 19 106.06 - 141.42: 0 141.42 - 176.77: 2 Dihedral angle restraints: 19335 sinusoidal: 10021 harmonic: 9314 Sorted by residual: dihedral pdb=" C4' DT F 61 " pdb=" C3' DT F 61 " pdb=" O3' DT F 61 " pdb=" P DG F 62 " ideal model delta sinusoidal sigma weight residual -140.00 36.77 -176.77 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC F -47 " pdb=" C3' DC F -47 " pdb=" O3' DC F -47 " pdb=" P DG F -46 " ideal model delta sinusoidal sigma weight residual 220.00 70.04 149.96 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CA ALA A 523 " pdb=" C ALA A 523 " pdb=" N ASN A 524 " pdb=" CA ASN A 524 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 19332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3047 0.028 - 0.056: 1328 0.056 - 0.083: 471 0.083 - 0.111: 287 0.111 - 0.139: 92 Chirality restraints: 5225 Sorted by residual: chirality pdb=" CA ILE D 78 " pdb=" N ILE D 78 " pdb=" C ILE D 78 " pdb=" CB ILE D 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 78 " pdb=" N ILE B 78 " pdb=" C ILE B 78 " pdb=" CB ILE B 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE B 320 " pdb=" N ILE B 320 " pdb=" C ILE B 320 " pdb=" CB ILE B 320 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 5222 not shown) Planarity restraints: 4885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG E -17 " -0.022 2.00e-02 2.50e+03 9.34e-03 2.62e+00 pdb=" N9 DG E -17 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG E -17 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG E -17 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG E -17 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG E -17 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E -17 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG E -17 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG E -17 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG E -17 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG E -17 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG E -17 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA E -25 " -0.020 2.00e-02 2.50e+03 9.04e-03 2.25e+00 pdb=" N9 DA E -25 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA E -25 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA E -25 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA E -25 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA E -25 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA E -25 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA E -25 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA E -25 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA E -25 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA E -25 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 327 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO D 328 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " 0.020 5.00e-02 4.00e+02 ... (remaining 4882 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5206 2.77 - 3.31: 27888 3.31 - 3.84: 52375 3.84 - 4.37: 59421 4.37 - 4.90: 100313 Nonbonded interactions: 245203 Sorted by model distance: nonbonded pdb=" OG1 THR C 799 " pdb=" OG1 THR C 803 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 184 " pdb=" OD1 ASP B 214 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR C 777 " pdb=" OD1 ASN C 780 " model vdw 2.282 3.040 nonbonded pdb=" O LEU A 320 " pdb=" OG1 THR A 324 " model vdw 2.284 3.040 nonbonded pdb=" NH1 ARG C 561 " pdb=" OP1 DC E -35 " model vdw 2.290 3.120 ... (remaining 245198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 9 through 541 or resid 543 through 806)) selection = (chain 'D' and (resid 9 through 541 or resid 543 through 806)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 9.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.140 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 0.039 33070 Z= 0.329 Angle : 0.548 6.705 46080 Z= 0.471 Chirality : 0.042 0.139 5225 Planarity : 0.003 0.036 4885 Dihedral : 18.686 176.773 13349 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % 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: 0.74 (0.15), residues: 3227 helix: 2.63 (0.16), residues: 1116 sheet: 0.79 (0.22), residues: 643 loop : -1.44 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 779 TYR 0.011 0.001 TYR A 266 PHE 0.010 0.001 PHE D 285 TRP 0.007 0.001 TRP D 629 HIS 0.004 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.33 (33070) covalent geometry : angle 0.54837 / 0.47 (46080) hydrogen bonds : bond 0.18412 / 12.53 ( 1511) hydrogen bonds : angle 5.56503 / 3.86 ( 3948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: D 56 CYS cc_start: 0.6268 (m) cc_final: 0.6029 (m) outliers start: 5 outliers final: 4 residues processed: 105 average time/residue: 0.9793 time to fit residues: 117.7330 Evaluate side-chains 90 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN C 780 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.038647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.030053 restraints weight = 224421.204| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.39 r_work: 0.3092 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33070 Z= 0.163 Angle : 0.541 9.064 46080 Z= 0.320 Chirality : 0.043 0.238 5225 Planarity : 0.004 0.079 4885 Dihedral : 23.627 173.197 7104 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.63 % Allowed : 4.64 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.15), residues: 3227 helix: 2.61 (0.16), residues: 1152 sheet: 0.76 (0.22), residues: 635 loop : -1.38 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 76 TYR 0.013 0.001 TYR D 528 PHE 0.014 0.001 PHE D 243 TRP 0.011 0.001 TRP B 258 HIS 0.006 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (33070) covalent geometry : angle 0.54065 / 0.32 (46080) hydrogen bonds : bond 0.05984 / 3.99 ( 1511) hydrogen bonds : angle 4.26751 / 2.97 ( 3948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 95 average time/residue: 0.9142 time to fit residues: 100.5559 Evaluate side-chains 90 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 32 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 344 optimal weight: 20.0000 chunk 226 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 552 GLN B 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.037904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.029360 restraints weight = 223723.520| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.49 r_work: 0.3039 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33070 Z= 0.222 Angle : 0.576 9.370 46080 Z= 0.334 Chirality : 0.045 0.248 5225 Planarity : 0.004 0.042 4885 Dihedral : 23.800 171.890 7100 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.55 % Allowed : 5.23 % Favored : 94.21 % 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: 0.63 (0.15), residues: 3227 helix: 2.51 (0.15), residues: 1149 sheet: 0.73 (0.22), residues: 625 loop : -1.56 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 596 TYR 0.014 0.001 TYR A 266 PHE 0.011 0.001 PHE D 169 TRP 0.010 0.001 TRP D 170 HIS 0.011 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (33070) covalent geometry : angle 0.57622 / 0.33 (46080) hydrogen bonds : bond 0.07101 / 4.72 ( 1511) hydrogen bonds : angle 4.12358 / 2.88 ( 3948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8381 (ptm-80) REVERT: D 597 MET cc_start: 0.9268 (ptp) cc_final: 0.8946 (ptm) REVERT: D 652 HIS cc_start: 0.8956 (t70) cc_final: 0.8608 (t-90) outliers start: 15 outliers final: 3 residues processed: 97 average time/residue: 0.8762 time to fit residues: 98.4953 Evaluate side-chains 92 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 167 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 338 optimal weight: 30.0000 chunk 228 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 336 optimal weight: 30.0000 chunk 280 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 281 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.038502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.030019 restraints weight = 223445.148| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.39 r_work: 0.3080 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33070 Z= 0.130 Angle : 0.507 8.628 46080 Z= 0.298 Chirality : 0.042 0.248 5225 Planarity : 0.003 0.040 4885 Dihedral : 23.768 172.179 7100 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.77 % Allowed : 5.82 % Favored : 93.40 % 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: 0.81 (0.15), residues: 3227 helix: 2.65 (0.15), residues: 1149 sheet: 0.77 (0.21), residues: 637 loop : -1.44 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 426 TYR 0.011 0.001 TYR A 266 PHE 0.012 0.001 PHE D 243 TRP 0.010 0.001 TRP D 170 HIS 0.006 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (33070) covalent geometry : angle 0.50750 / 0.30 (46080) hydrogen bonds : bond 0.05208 / 3.45 ( 1511) hydrogen bonds : angle 3.88756 / 2.71 ( 3948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 627 GLN cc_start: 0.8434 (pm20) cc_final: 0.8216 (pp30) REVERT: C 779 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8159 (ptt-90) REVERT: D 597 MET cc_start: 0.9222 (ptp) cc_final: 0.8827 (ptm) REVERT: D 652 HIS cc_start: 0.8950 (t70) cc_final: 0.8631 (t-90) outliers start: 21 outliers final: 4 residues processed: 105 average time/residue: 0.8453 time to fit residues: 103.7389 Evaluate side-chains 94 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 272 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 282 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.038367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.029707 restraints weight = 223952.326| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.38 r_work: 0.3077 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33070 Z= 0.149 Angle : 0.516 10.292 46080 Z= 0.302 Chirality : 0.042 0.243 5225 Planarity : 0.004 0.040 4885 Dihedral : 23.756 172.548 7100 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.37 % Allowed : 6.38 % Favored : 93.25 % 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: 0.82 (0.15), residues: 3227 helix: 2.69 (0.15), residues: 1150 sheet: 0.81 (0.21), residues: 628 loop : -1.46 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 426 TYR 0.010 0.001 TYR A 266 PHE 0.011 0.001 PHE D 169 TRP 0.010 0.001 TRP D 170 HIS 0.006 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (33070) covalent geometry : angle 0.51635 / 0.30 (46080) hydrogen bonds : bond 0.05492 / 3.64 ( 1511) hydrogen bonds : angle 3.84845 / 2.68 ( 3948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8165 (ptt-90) REVERT: D 597 MET cc_start: 0.9197 (ptp) cc_final: 0.8861 (ptm) REVERT: D 652 HIS cc_start: 0.8953 (t70) cc_final: 0.8657 (t-90) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 0.9050 time to fit residues: 99.3468 Evaluate side-chains 93 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 200 optimal weight: 0.9980 chunk 334 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 242 optimal weight: 3.9990 chunk 295 optimal weight: 0.2980 chunk 271 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.038875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.030402 restraints weight = 223453.832| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.32 r_work: 0.3112 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 33070 Z= 0.112 Angle : 0.491 10.101 46080 Z= 0.287 Chirality : 0.041 0.249 5225 Planarity : 0.003 0.066 4885 Dihedral : 23.722 173.414 7100 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.48 % Allowed : 6.86 % Favored : 92.66 % 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: 0.96 (0.15), residues: 3227 helix: 2.80 (0.15), residues: 1150 sheet: 0.81 (0.21), residues: 642 loop : -1.36 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 599 TYR 0.009 0.001 TYR A 266 PHE 0.010 0.001 PHE D 243 TRP 0.009 0.001 TRP D 170 HIS 0.004 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.11 (33070) covalent geometry : angle 0.49060 / 0.29 (46080) hydrogen bonds : bond 0.04510 / 2.98 ( 1511) hydrogen bonds : angle 3.71075 / 2.58 ( 3948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 627 GLN cc_start: 0.8416 (pm20) cc_final: 0.8192 (pp30) REVERT: C 779 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8252 (ptt-90) REVERT: D 597 MET cc_start: 0.9126 (ptp) cc_final: 0.8841 (ptm) REVERT: D 652 HIS cc_start: 0.8949 (t70) cc_final: 0.8653 (t-90) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 0.8015 time to fit residues: 90.9467 Evaluate side-chains 93 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 34 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 269 optimal weight: 0.4980 chunk 344 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 345 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.038224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.029670 restraints weight = 223888.900| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.32 r_work: 0.3071 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33070 Z= 0.177 Angle : 0.533 9.765 46080 Z= 0.309 Chirality : 0.043 0.243 5225 Planarity : 0.004 0.039 4885 Dihedral : 23.744 173.042 7100 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.44 % Allowed : 7.15 % Favored : 92.41 % 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: 0.85 (0.15), residues: 3227 helix: 2.73 (0.16), residues: 1152 sheet: 0.84 (0.22), residues: 621 loop : -1.46 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 826 TYR 0.010 0.001 TYR C 21 PHE 0.013 0.001 PHE D 169 TRP 0.009 0.001 TRP B 258 HIS 0.007 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (33070) covalent geometry : angle 0.53301 / 0.31 (46080) hydrogen bonds : bond 0.05920 / 3.92 ( 1511) hydrogen bonds : angle 3.82325 / 2.67 ( 3948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8165 (ptt-90) REVERT: D 597 MET cc_start: 0.9175 (ptp) cc_final: 0.8909 (ptm) REVERT: D 652 HIS cc_start: 0.8919 (t70) cc_final: 0.8625 (t-90) outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 0.8149 time to fit residues: 89.9074 Evaluate side-chains 93 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 212 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 344 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 277 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.038179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.029514 restraints weight = 223569.881| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.37 r_work: 0.3067 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33070 Z= 0.171 Angle : 0.528 9.825 46080 Z= 0.306 Chirality : 0.043 0.228 5225 Planarity : 0.004 0.042 4885 Dihedral : 23.750 172.472 7100 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.44 % Allowed : 7.30 % Favored : 92.26 % 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: 0.83 (0.15), residues: 3227 helix: 2.71 (0.15), residues: 1149 sheet: 0.84 (0.22), residues: 620 loop : -1.48 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 426 TYR 0.010 0.001 TYR A 266 PHE 0.012 0.001 PHE D 169 TRP 0.010 0.001 TRP D 170 HIS 0.007 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (33070) covalent geometry : angle 0.52763 / 0.31 (46080) hydrogen bonds : bond 0.05780 / 3.82 ( 1511) hydrogen bonds : angle 3.81953 / 2.66 ( 3948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8156 (ptt-90) REVERT: D 597 MET cc_start: 0.9153 (ptp) cc_final: 0.8921 (ptm) REVERT: D 652 HIS cc_start: 0.8907 (t70) cc_final: 0.8602 (t-90) outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 0.8357 time to fit residues: 92.9754 Evaluate side-chains 93 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 248 optimal weight: 0.4980 chunk 201 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.038385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.029741 restraints weight = 222651.841| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.39 r_work: 0.3077 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33070 Z= 0.135 Angle : 0.506 9.894 46080 Z= 0.295 Chirality : 0.042 0.223 5225 Planarity : 0.003 0.040 4885 Dihedral : 23.743 172.753 7100 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.37 % Allowed : 7.34 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.89 (0.15), residues: 3227 helix: 2.77 (0.15), residues: 1149 sheet: 0.83 (0.21), residues: 633 loop : -1.45 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 426 TYR 0.009 0.001 TYR A 266 PHE 0.011 0.001 PHE D 169 TRP 0.010 0.001 TRP D 170 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (33070) covalent geometry : angle 0.50628 / 0.30 (46080) hydrogen bonds : bond 0.05265 / 3.48 ( 1511) hydrogen bonds : angle 3.76236 / 2.62 ( 3948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8168 (ptt-90) REVERT: C 795 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9102 (pp) REVERT: B 166 MET cc_start: 0.8818 (tmm) cc_final: 0.8604 (tmt) REVERT: D 597 MET cc_start: 0.9115 (ptp) cc_final: 0.8888 (ptm) REVERT: D 652 HIS cc_start: 0.8911 (t70) cc_final: 0.8606 (t-90) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.8388 time to fit residues: 92.6075 Evaluate side-chains 95 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 280 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 350 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.038234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.029558 restraints weight = 223628.646| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.40 r_work: 0.3067 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33070 Z= 0.159 Angle : 0.520 9.792 46080 Z= 0.301 Chirality : 0.042 0.228 5225 Planarity : 0.004 0.041 4885 Dihedral : 23.753 172.783 7100 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.33 % Allowed : 7.37 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.15), residues: 3227 helix: 2.74 (0.15), residues: 1149 sheet: 0.87 (0.22), residues: 620 loop : -1.48 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 426 TYR 0.010 0.001 TYR C 21 PHE 0.011 0.001 PHE D 169 TRP 0.010 0.001 TRP D 170 HIS 0.006 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (33070) covalent geometry : angle 0.51990 / 0.30 (46080) hydrogen bonds : bond 0.05629 / 3.73 ( 1511) hydrogen bonds : angle 3.78687 / 2.64 ( 3948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6454 Ramachandran restraints generated. 3227 Oldfield, 0 Emsley, 3227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8167 (ptt-90) REVERT: C 795 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9101 (pp) REVERT: B 166 MET cc_start: 0.8769 (tmm) cc_final: 0.8518 (tmt) REVERT: D 597 MET cc_start: 0.9124 (ptp) cc_final: 0.8891 (ptm) REVERT: D 652 HIS cc_start: 0.8899 (t70) cc_final: 0.8592 (t-90) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.8085 time to fit residues: 88.2484 Evaluate side-chains 94 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 389 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 338 optimal weight: 30.0000 chunk 242 optimal weight: 0.7980 chunk 348 optimal weight: 20.0000 chunk 292 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 294 optimal weight: 0.0970 chunk 262 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.038914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.030350 restraints weight = 224394.280| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.42 r_work: 0.3112 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33070 Z= 0.109 Angle : 0.483 10.046 46080 Z= 0.282 Chirality : 0.041 0.200 5225 Planarity : 0.003 0.037 4885 Dihedral : 23.712 173.636 7100 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.26 % Allowed : 7.48 % Favored : 92.26 % 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: 1.01 (0.15), residues: 3227 helix: 2.85 (0.15), residues: 1149 sheet: 0.83 (0.21), residues: 646 loop : -1.34 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 426 TYR 0.008 0.001 TYR A 266 PHE 0.010 0.001 PHE D 169 TRP 0.011 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.11 (33070) covalent geometry : angle 0.48334 / 0.28 (46080) hydrogen bonds : bond 0.04330 / 2.86 ( 1511) hydrogen bonds : angle 3.63446 / 2.53 ( 3948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16228.71 seconds wall clock time: 275 minutes 11.89 seconds (16511.89 seconds total)