Starting phenix.real_space_refine on Thu May 29 06:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gbv_51222/05_2025/9gbv_51222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gbv_51222/05_2025/9gbv_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_51222/05_2025/9gbv_51222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gbv_51222/05_2025/9gbv_51222.map" model { file = "/net/cci-nas-00/data/ceres_data/9gbv_51222/05_2025/9gbv_51222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gbv_51222/05_2025/9gbv_51222.cif" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 23.56, per 1000 atoms: 0.74 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: 8.09 Conformation dependent library (CDL) restraints added in 4.2 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: 12.93 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: 20.09 Time building geometry restraints manager: 9.35 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' DA E -18 " pdb=" O3' DA E -18 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" C3' DC F -47 " pdb=" O3' DC F -47 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.36e-01 bond pdb=" C3' DC F 31 " pdb=" C2' DC F 31 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.15e-01 bond pdb=" C3' DC E -31 " pdb=" C2' DC E -31 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.10e-01 bond pdb=" C3' DA E -18 " pdb=" C2' DA E -18 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.08e-01 ... (remaining 33065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 45208 1.34 - 2.68: 775 2.68 - 4.02: 85 4.02 - 5.36: 7 5.36 - 6.71: 5 Bond angle restraints: 46080 Sorted by residual: angle pdb=" N VAL D 345 " pdb=" CA VAL D 345 " pdb=" C VAL D 345 " ideal model delta sigma weight residual 112.96 109.56 3.40 1.00e+00 1.00e+00 1.15e+01 angle pdb=" N ILE B 10 " pdb=" CA ILE B 10 " pdb=" C ILE B 10 " ideal model delta sigma weight residual 113.39 109.53 3.86 1.47e+00 4.63e-01 6.90e+00 angle pdb=" C3' DC F 72 " pdb=" C2' DC F 72 " pdb=" C1' DC F 72 " ideal model delta sigma weight residual 101.60 97.66 3.94 1.50e+00 4.44e-01 6.89e+00 angle pdb=" N VAL C 784 " pdb=" CA VAL C 784 " pdb=" C VAL C 784 " ideal model delta sigma weight residual 112.96 110.34 2.62 1.00e+00 1.00e+00 6.89e+00 angle pdb=" N GLY C 31 " pdb=" CA GLY C 31 " pdb=" C GLY C 31 " ideal model delta sigma weight residual 113.18 118.69 -5.51 2.37e+00 1.78e-01 5.40e+00 ... (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: 3464 0.028 - 0.056: 1133 0.056 - 0.083: 325 0.083 - 0.111: 219 0.111 - 0.139: 84 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: 0.010 Normalize map: mean=0, sd=1: 13.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.320 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 91.530 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.002 0.039 33070 Z= 0.108 Angle : 0.441 6.705 46080 Z= 0.256 Chirality : 0.037 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 : 3.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (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 TRP 0.007 0.001 TRP D 629 HIS 0.004 0.001 HIS D 281 PHE 0.010 0.001 PHE D 285 TYR 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG A 779 Details of bonding type rmsd hydrogen bonds : bond 0.18412 ( 1511) hydrogen bonds : angle 5.56503 ( 3948) covalent geometry : bond 0.00221 (33070) covalent geometry : angle 0.44144 (46080) *********************** 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 : 3.083 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: 2.0195 time to fit residues: 242.5386 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 : 3.173 ------------------------------------------------------------------------------- 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 297 optimal weight: 0.7980 chunk 266 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 0.4980 chunk 205 optimal weight: 0.7980 chunk 319 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN C 552 GLN C 780 ASN B 281 HIS B 364 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.038903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.030309 restraints weight = 223673.138| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.37 r_work: 0.3108 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 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 = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33070 Z= 0.134 Angle : 0.489 8.622 46080 Z= 0.284 Chirality : 0.039 0.152 5225 Planarity : 0.004 0.062 4885 Dihedral : 23.487 176.388 7104 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.59 % Allowed : 4.64 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3227 helix: 2.68 (0.16), residues: 1154 sheet: 0.80 (0.22), residues: 640 loop : -1.31 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 258 HIS 0.005 0.001 HIS D 281 PHE 0.009 0.001 PHE D 169 TYR 0.011 0.001 TYR A 266 ARG 0.014 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.05187 ( 1511) hydrogen bonds : angle 4.13999 ( 3948) covalent geometry : bond 0.00284 (33070) covalent geometry : angle 0.48893 (46080) *********************** 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 105 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 3.032 Fit side-chains revert: symmetry clash REVERT: D 597 MET cc_start: 0.9248 (ptp) cc_final: 0.8959 (ptm) outliers start: 16 outliers final: 2 residues processed: 95 average time/residue: 1.8187 time to fit residues: 201.5305 Evaluate side-chains 88 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 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 52 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 270 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.038699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.030148 restraints weight = 224598.849| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.34 r_work: 0.3094 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 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 = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33070 Z= 0.143 Angle : 0.487 9.262 46080 Z= 0.282 Chirality : 0.039 0.142 5225 Planarity : 0.003 0.042 4885 Dihedral : 23.474 175.993 7100 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.77 % Allowed : 4.79 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3227 helix: 2.71 (0.16), residues: 1155 sheet: 0.80 (0.22), residues: 636 loop : -1.36 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 258 HIS 0.006 0.001 HIS D 281 PHE 0.011 0.001 PHE D 169 TYR 0.012 0.001 TYR A 266 ARG 0.010 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.05118 ( 1511) hydrogen bonds : angle 3.85926 ( 3948) covalent geometry : bond 0.00316 (33070) covalent geometry : angle 0.48671 (46080) *********************** 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 113 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 3.426 Fit side-chains revert: symmetry clash REVERT: A 627 GLN cc_start: 0.8457 (pm20) cc_final: 0.8251 (pp30) REVERT: D 552 MET cc_start: 0.8916 (tpt) cc_final: 0.8705 (tpp) REVERT: D 597 MET cc_start: 0.9250 (ptp) cc_final: 0.8932 (ptm) REVERT: D 652 HIS cc_start: 0.8959 (t70) cc_final: 0.8641 (t-90) outliers start: 21 outliers final: 4 residues processed: 105 average time/residue: 1.6308 time to fit residues: 201.1542 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 : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain D residue 297 MET 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 221 optimal weight: 3.9990 chunk 181 optimal weight: 0.0770 chunk 115 optimal weight: 0.9980 chunk 173 optimal weight: 0.0670 chunk 80 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.039615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.031196 restraints weight = 226115.622| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.31 r_work: 0.3146 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33070 Z= 0.104 Angle : 0.461 10.388 46080 Z= 0.265 Chirality : 0.038 0.140 5225 Planarity : 0.003 0.040 4885 Dihedral : 23.408 177.562 7100 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.37 % Allowed : 5.90 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3227 helix: 2.83 (0.15), residues: 1155 sheet: 0.81 (0.21), residues: 652 loop : -1.25 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.003 0.000 HIS D 281 PHE 0.010 0.001 PHE D 285 TYR 0.007 0.001 TYR A 266 ARG 0.007 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1511) hydrogen bonds : angle 3.61317 ( 3948) covalent geometry : bond 0.00212 (33070) covalent geometry : angle 0.46108 (46080) *********************** 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 100 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 3.232 Fit side-chains revert: symmetry clash REVERT: D 166 MET cc_start: 0.8341 (tmm) cc_final: 0.8106 (tmt) REVERT: D 597 MET cc_start: 0.9156 (ptp) cc_final: 0.8770 (ptm) REVERT: D 652 HIS cc_start: 0.8960 (t70) cc_final: 0.8660 (t-90) outliers start: 10 outliers final: 2 residues processed: 95 average time/residue: 1.8560 time to fit residues: 204.4250 Evaluate side-chains 89 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 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 170 optimal weight: 0.0970 chunk 158 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 2 optimal weight: 0.1980 chunk 247 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 322 optimal weight: 10.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.038263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.029704 restraints weight = 222394.667| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.30 r_work: 0.3068 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33070 Z= 0.199 Angle : 0.522 10.178 46080 Z= 0.301 Chirality : 0.040 0.150 5225 Planarity : 0.004 0.041 4885 Dihedral : 23.449 176.112 7100 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.52 % Allowed : 5.82 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3227 helix: 2.76 (0.16), residues: 1153 sheet: 0.90 (0.22), residues: 629 loop : -1.42 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 258 HIS 0.007 0.001 HIS B 281 PHE 0.011 0.001 PHE D 169 TYR 0.011 0.001 TYR A 605 ARG 0.009 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.06066 ( 1511) hydrogen bonds : angle 3.81714 ( 3948) covalent geometry : bond 0.00460 (33070) covalent geometry : angle 0.52216 (46080) *********************** 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 104 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 3.095 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8388 (ptm-80) REVERT: D 597 MET cc_start: 0.9240 (ptp) cc_final: 0.8936 (ptm) REVERT: D 652 HIS cc_start: 0.8938 (t70) cc_final: 0.8644 (t-90) outliers start: 14 outliers final: 6 residues processed: 96 average time/residue: 1.7426 time to fit residues: 194.7602 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 : 3.051 ------------------------------------------------------------------------------- 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 B residue 99 HIS Chi-restraints excluded: chain D residue 56 CYS 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 336 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 147 optimal weight: 6.9990 chunk 243 optimal weight: 0.0570 chunk 270 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN ** A 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.038498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.029869 restraints weight = 223341.060| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.38 r_work: 0.3083 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 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 = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33070 Z= 0.148 Angle : 0.492 9.631 46080 Z= 0.285 Chirality : 0.039 0.145 5225 Planarity : 0.003 0.039 4885 Dihedral : 23.450 175.873 7100 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.41 % Allowed : 6.60 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3227 helix: 2.79 (0.15), residues: 1151 sheet: 0.88 (0.22), residues: 629 loop : -1.39 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 170 HIS 0.006 0.001 HIS D 281 PHE 0.011 0.001 PHE D 169 TYR 0.010 0.001 TYR A 266 ARG 0.006 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 1511) hydrogen bonds : angle 3.73956 ( 3948) covalent geometry : bond 0.00330 (33070) covalent geometry : angle 0.49166 (46080) *********************** 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 99 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 3.329 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8164 (ptt-90) REVERT: C 795 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9098 (pp) REVERT: D 597 MET cc_start: 0.9243 (ptp) cc_final: 0.8918 (ptm) REVERT: D 652 HIS cc_start: 0.8907 (t70) cc_final: 0.8588 (t-90) outliers start: 11 outliers final: 6 residues processed: 95 average time/residue: 1.8188 time to fit residues: 201.1361 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 : 3.362 ------------------------------------------------------------------------------- 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 C residue 795 ILE Chi-restraints excluded: chain D residue 56 CYS 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 179 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN A 627 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.037601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.028878 restraints weight = 223975.032| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.35 r_work: 0.3037 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 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 = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 33070 Z= 0.273 Angle : 0.577 9.283 46080 Z= 0.332 Chirality : 0.043 0.148 5225 Planarity : 0.004 0.045 4885 Dihedral : 23.559 174.405 7100 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.48 % Allowed : 6.71 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3227 helix: 2.54 (0.15), residues: 1149 sheet: 0.79 (0.22), residues: 623 loop : -1.56 (0.14), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 258 HIS 0.009 0.001 HIS B 281 PHE 0.013 0.002 PHE B 41 TYR 0.012 0.001 TYR A 122 ARG 0.005 0.001 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.07264 ( 1511) hydrogen bonds : angle 4.02526 ( 3948) covalent geometry : bond 0.00640 (33070) covalent geometry : angle 0.57717 (46080) *********************** 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 101 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8664 (tmm) cc_final: 0.8454 (tmt) REVERT: D 652 HIS cc_start: 0.8911 (t70) cc_final: 0.8617 (t-90) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 1.8104 time to fit residues: 202.7767 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 : 3.516 ------------------------------------------------------------------------------- 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 779 ARG Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 83 HIS 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 27 optimal weight: 0.3980 chunk 331 optimal weight: 7.9990 chunk 336 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 181 optimal weight: 0.0980 chunk 322 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 256 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.038781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.030298 restraints weight = 225558.888| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.36 r_work: 0.3100 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 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 = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33070 Z= 0.118 Angle : 0.481 9.664 46080 Z= 0.278 Chirality : 0.038 0.144 5225 Planarity : 0.003 0.038 4885 Dihedral : 23.488 176.179 7100 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.29 % Allowed : 6.93 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3227 helix: 2.78 (0.15), residues: 1150 sheet: 0.78 (0.21), residues: 643 loop : -1.38 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 170 HIS 0.005 0.001 HIS D 281 PHE 0.011 0.001 PHE D 169 TYR 0.007 0.001 TYR A 266 ARG 0.005 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 1511) hydrogen bonds : angle 3.68376 ( 3948) covalent geometry : bond 0.00244 (33070) covalent geometry : angle 0.48132 (46080) *********************** 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 96 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 3.262 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8221 (ptt-90) REVERT: D 652 HIS cc_start: 0.8886 (t70) cc_final: 0.8595 (t-90) outliers start: 8 outliers final: 4 residues processed: 92 average time/residue: 1.8804 time to fit residues: 202.1615 Evaluate side-chains 91 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain D residue 56 CYS 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 287 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.0870 chunk 275 optimal weight: 0.9990 chunk 320 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.039102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.030738 restraints weight = 225526.818| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.24 r_work: 0.3126 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33070 Z= 0.115 Angle : 0.466 9.310 46080 Z= 0.269 Chirality : 0.038 0.140 5225 Planarity : 0.003 0.039 4885 Dihedral : 23.408 178.016 7100 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.26 % Allowed : 7.19 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3227 helix: 2.88 (0.15), residues: 1154 sheet: 0.82 (0.21), residues: 650 loop : -1.30 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 170 HIS 0.004 0.001 HIS D 281 PHE 0.013 0.001 PHE D 285 TYR 0.007 0.001 TYR C 21 ARG 0.007 0.000 ARG D 599 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 1511) hydrogen bonds : angle 3.55256 ( 3948) covalent geometry : bond 0.00245 (33070) covalent geometry : angle 0.46616 (46080) *********************** 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 94 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 3.183 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8307 (ptt-90) REVERT: D 389 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.6174 (ppt90) REVERT: D 652 HIS cc_start: 0.8946 (t70) cc_final: 0.8646 (t-90) outliers start: 7 outliers final: 2 residues processed: 92 average time/residue: 1.7407 time to fit residues: 187.0401 Evaluate side-chains 91 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 151 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 314 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.038166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.029498 restraints weight = 223336.621| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.44 r_work: 0.3055 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 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 = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33070 Z= 0.200 Angle : 0.523 9.675 46080 Z= 0.301 Chirality : 0.040 0.170 5225 Planarity : 0.004 0.070 4885 Dihedral : 23.451 176.195 7100 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.22 % Allowed : 7.22 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3227 helix: 2.75 (0.16), residues: 1152 sheet: 0.84 (0.22), residues: 630 loop : -1.47 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 258 HIS 0.007 0.001 HIS B 281 PHE 0.011 0.001 PHE D 169 TYR 0.010 0.001 TYR A 266 ARG 0.019 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.05906 ( 1511) hydrogen bonds : angle 3.76064 ( 3948) covalent geometry : bond 0.00462 (33070) covalent geometry : angle 0.52325 (46080) ********************** 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 92 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 3.180 Fit side-chains revert: symmetry clash REVERT: C 779 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8167 (ptt-90) REVERT: D 389 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.5888 (ppt90) REVERT: D 652 HIS cc_start: 0.8893 (t70) cc_final: 0.8607 (t-90) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 1.8301 time to fit residues: 191.7051 Evaluate side-chains 91 residues out of total 2711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain D residue 56 CYS 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 195 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 225 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 348 optimal weight: 6.9990 chunk 298 optimal weight: 0.0870 chunk 254 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.038304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.029733 restraints weight = 222663.121| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.39 r_work: 0.3071 rms_B_bonded: 3.24 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 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33070 Z= 0.161 Angle : 0.504 9.225 46080 Z= 0.290 Chirality : 0.039 0.147 5225 Planarity : 0.004 0.097 4885 Dihedral : 23.464 176.043 7100 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3227 helix: 2.74 (0.15), residues: 1152 sheet: 0.85 (0.22), residues: 623 loop : -1.43 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 170 HIS 0.006 0.001 HIS B 281 PHE 0.011 0.001 PHE D 169 TYR 0.011 0.001 TYR A 266 ARG 0.020 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 1511) hydrogen bonds : angle 3.73143 ( 3948) covalent geometry : bond 0.00364 (33070) covalent geometry : angle 0.50441 (46080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32491.34 seconds wall clock time: 558 minutes 57.51 seconds (33537.51 seconds total)