Starting phenix.real_space_refine on Fri Sep 27 23:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/09_2024/7vz3_32219.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/09_2024/7vz3_32219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/09_2024/7vz3_32219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/09_2024/7vz3_32219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/09_2024/7vz3_32219.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/09_2024/7vz3_32219.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10985 2.51 5 N 2950 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17415 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5798 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 720} Chain: "B" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5819 Classifications: {'peptide': 754} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 723} Chain: "C" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5798 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 720} Time building chain proxies: 10.50, per 1000 atoms: 0.60 Number of scatterers: 17415 At special positions: 0 Unit cell: (94.569, 93.482, 192.399, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3414 8.00 N 2950 7.00 C 10985 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: 4.22 Conformation dependent library (CDL) restraints added in 2.3 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 24 sheets defined 20.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 155 through 182 removed outlier: 3.559A pdb=" N ALA A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 removed outlier: 4.062A pdb=" N VAL A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 301 through 316 Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 643 through 646 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 662 through 665 Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 828 through 832 Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 886 through 902 Processing helix chain 'B' and resid 153 through 183 removed outlier: 4.118A pdb=" N ASN B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'B' and resid 662 through 665 Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 741 through 746 Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 823 through 827 Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 886 through 902 Processing helix chain 'C' and resid 156 through 181 removed outlier: 3.701A pdb=" N ALA C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 301 through 316 Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 653 through 659 Processing helix chain 'C' and resid 662 through 665 Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 784 through 788 removed outlier: 3.612A pdb=" N PHE C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 827 Processing helix chain 'C' and resid 828 through 832 Processing helix chain 'C' and resid 862 through 867 Processing helix chain 'C' and resid 885 through 902 removed outlier: 4.013A pdb=" N ASN C 889 " --> pdb=" O VAL C 885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.482A pdb=" N PHE A 274 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 319 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS A 467 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 596 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN A 548 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.235A pdb=" N GLY A 324 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR A 351 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 326 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR A 348 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 428 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE A 463 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 430 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 537 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN A 511 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 539 " --> pdb=" O GLN A 511 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 513 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 6.383A pdb=" N LEU A 334 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA A 364 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASN A 392 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET A 366 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 389 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TYR A 418 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 391 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP A 415 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE A 444 " --> pdb=" O TRP A 415 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 417 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU A 446 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 419 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLN A 441 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN A 501 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N CYS A 500 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 528 " --> pdb=" O CYS A 500 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA A 577 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER A 527 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 579 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA A 529 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER A 581 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 531 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA A 576 " --> pdb=" O THR A 601 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS A 603 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 578 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET A 605 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 580 " --> pdb=" O MET A 605 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TRP A 627 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 602 " --> pdb=" O TRP A 627 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AA6, first strand: chain 'A' and resid 795 through 801 removed outlier: 3.507A pdb=" N TYR A 751 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR A 757 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE A 838 " --> pdb=" O THR A 757 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 839 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A 672 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 841 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AA8, first strand: chain 'A' and resid 727 through 732 removed outlier: 3.943A pdb=" N LEU A 727 " --> pdb=" O PHE A 813 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.887A pdb=" N SER B 667 " --> pdb=" O TYR B 845 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR B 845 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU B 669 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 843 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 671 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 838 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 757 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 751 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 220 through 225 removed outlier: 5.615A pdb=" N SER B 225 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 239 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.547A pdb=" N PHE B 274 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ARG B 434 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 408 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLN B 436 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 410 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA B 435 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 467 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N ASP B 543 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N LYS B 595 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B 545 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LYS B 597 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 547 " --> pdb=" O LYS B 597 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.069A pdb=" N THR B 348 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 405 " --> pdb=" O HIS B 431 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 428 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE B 463 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B 430 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 460 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 513 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B 462 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 537 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN B 511 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 539 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 513 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 334 through 336 removed outlier: 6.342A pdb=" N LEU B 334 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA B 364 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASN B 392 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET B 366 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE B 417 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B 392 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 419 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B 442 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLN B 441 " --> pdb=" O GLY B 499 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN B 501 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N CYS B 500 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 528 " --> pdb=" O CYS B 500 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA B 577 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 601 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 727 through 732 removed outlier: 3.922A pdb=" N LEU B 727 " --> pdb=" O PHE B 813 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 858 through 859 removed outlier: 6.421A pdb=" N ILE C 841 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN C 672 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 839 " --> pdb=" O ASN C 672 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE C 838 " --> pdb=" O THR C 757 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 757 " --> pdb=" O PHE C 838 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 751 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 225 removed outlier: 5.473A pdb=" N SER C 225 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY C 239 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.576A pdb=" N PHE C 274 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS C 467 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ASP C 543 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N LYS C 595 " --> pdb=" O ASP C 543 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU C 545 " --> pdb=" O LYS C 595 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LYS C 597 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 547 " --> pdb=" O LYS C 597 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.031A pdb=" N THR C 348 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 405 " --> pdb=" O HIS C 431 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 428 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 463 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 430 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 460 " --> pdb=" O GLN C 511 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE C 513 " --> pdb=" O VAL C 460 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 462 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER C 536 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 334 through 336 removed outlier: 6.402A pdb=" N LEU C 334 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE C 391 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN C 367 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE C 393 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS C 389 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR C 418 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 391 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP C 415 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE C 444 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE C 417 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU C 446 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 419 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLN C 441 " --> pdb=" O GLY C 499 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLN C 501 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS C 500 " --> pdb=" O LEU C 528 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR C 530 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 502 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR C 532 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE C 504 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ALA C 577 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER C 527 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL C 579 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA C 529 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER C 581 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 531 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 576 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 603 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 578 " --> pdb=" O LYS C 603 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N MET C 605 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 580 " --> pdb=" O MET C 605 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TRP C 627 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 602 " --> pdb=" O TRP C 627 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 480 through 482 Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AC6, first strand: chain 'C' and resid 727 through 732 removed outlier: 3.974A pdb=" N LEU C 727 " --> pdb=" O PHE C 813 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5547 1.34 - 1.47: 4710 1.47 - 1.59: 7464 1.59 - 1.72: 3 1.72 - 1.85: 105 Bond restraints: 17829 Sorted by residual: bond pdb=" CB GLN C 177 " pdb=" CG GLN C 177 " ideal model delta sigma weight residual 1.520 1.612 -0.092 3.00e-02 1.11e+03 9.42e+00 bond pdb=" CB ILE C 466 " pdb=" CG2 ILE C 466 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.28e+00 bond pdb=" CG LEU A 311 " pdb=" CD1 LEU A 311 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.03e+00 bond pdb=" CB ARG A 267 " pdb=" CG ARG A 267 " ideal model delta sigma weight residual 1.520 1.436 0.084 3.00e-02 1.11e+03 7.81e+00 bond pdb=" CB THR A 325 " pdb=" CG2 THR A 325 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.35e+00 ... (remaining 17824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 22843 2.17 - 4.34: 1182 4.34 - 6.51: 158 6.51 - 8.67: 22 8.67 - 10.84: 1 Bond angle restraints: 24206 Sorted by residual: angle pdb=" N ASN B 607 " pdb=" CA ASN B 607 " pdb=" C ASN B 607 " ideal model delta sigma weight residual 112.24 118.64 -6.40 1.28e+00 6.10e-01 2.50e+01 angle pdb=" N ASN B 468 " pdb=" CA ASN B 468 " pdb=" C ASN B 468 " ideal model delta sigma weight residual 109.06 116.74 -7.68 1.70e+00 3.46e-01 2.04e+01 angle pdb=" N ASN B 606 " pdb=" CA ASN B 606 " pdb=" C ASN B 606 " ideal model delta sigma weight residual 111.39 117.57 -6.18 1.38e+00 5.25e-01 2.00e+01 angle pdb=" C PHE B 904 " pdb=" N MET B 905 " pdb=" CA MET B 905 " ideal model delta sigma weight residual 121.70 129.22 -7.52 1.80e+00 3.09e-01 1.74e+01 angle pdb=" N ALA A 745 " pdb=" CA ALA A 745 " pdb=" C ALA A 745 " ideal model delta sigma weight residual 111.28 115.77 -4.49 1.09e+00 8.42e-01 1.70e+01 ... (remaining 24201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 9668 17.77 - 35.54: 637 35.54 - 53.30: 87 53.30 - 71.07: 26 71.07 - 88.84: 17 Dihedral angle restraints: 10435 sinusoidal: 3961 harmonic: 6474 Sorted by residual: dihedral pdb=" C VAL B 885 " pdb=" N VAL B 885 " pdb=" CA VAL B 885 " pdb=" CB VAL B 885 " ideal model delta harmonic sigma weight residual -122.00 -134.95 12.95 0 2.50e+00 1.60e-01 2.68e+01 dihedral pdb=" N VAL B 885 " pdb=" C VAL B 885 " pdb=" CA VAL B 885 " pdb=" CB VAL B 885 " ideal model delta harmonic sigma weight residual 123.40 136.08 -12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" CA ASP C 847 " pdb=" C ASP C 847 " pdb=" N LEU C 848 " pdb=" CA LEU C 848 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 10432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2135 0.081 - 0.162: 440 0.162 - 0.243: 47 0.243 - 0.324: 5 0.324 - 0.405: 4 Chirality restraints: 2631 Sorted by residual: chirality pdb=" CA VAL B 885 " pdb=" N VAL B 885 " pdb=" C VAL B 885 " pdb=" CB VAL B 885 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA ASN B 607 " pdb=" N ASN B 607 " pdb=" C ASN B 607 " pdb=" CB ASN B 607 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA LEU C 746 " pdb=" N LEU C 746 " pdb=" C LEU C 746 " pdb=" CB LEU C 746 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2628 not shown) Planarity restraints: 3191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 782 " -0.064 2.00e-02 2.50e+03 4.06e-02 4.13e+01 pdb=" CG TRP C 782 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP C 782 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 782 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 782 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 782 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 782 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 782 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 782 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 782 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 782 " 0.062 2.00e-02 2.50e+03 4.02e-02 4.04e+01 pdb=" CG TRP A 782 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TRP A 782 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 782 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 782 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 782 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 782 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 782 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 782 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 782 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 782 " 0.058 2.00e-02 2.50e+03 3.90e-02 3.81e+01 pdb=" CG TRP B 782 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TRP B 782 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP B 782 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP B 782 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 782 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 782 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 782 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 782 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 782 " 0.007 2.00e-02 2.50e+03 ... (remaining 3188 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1736 2.74 - 3.28: 16575 3.28 - 3.82: 28578 3.82 - 4.36: 38042 4.36 - 4.90: 64039 Nonbonded interactions: 148970 Sorted by model distance: nonbonded pdb=" O SER B 648 " pdb=" OH TYR B 751 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG A 395 " pdb=" O GLU A 423 " model vdw 2.222 3.120 nonbonded pdb=" O ALA A 161 " pdb=" OG SER A 164 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG B 395 " pdb=" O GLU B 423 " model vdw 2.239 3.120 nonbonded pdb=" OG SER B 383 " pdb=" OG SER B 385 " model vdw 2.250 3.040 ... (remaining 148965 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 'B' and resid 155 through 905) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.970 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0205 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 : 0.009 0.098 17829 Z= 0.617 Angle : 1.083 10.842 24206 Z= 0.627 Chirality : 0.066 0.405 2631 Planarity : 0.007 0.048 3191 Dihedral : 12.804 88.841 6319 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 0.26 % Allowed : 2.31 % Favored : 97.42 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 10.00 % 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: -1.44 (0.17), residues: 2250 helix: -0.07 (0.27), residues: 374 sheet: -0.52 (0.20), residues: 699 loop : -1.51 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.008 TRP C 782 HIS 0.013 0.003 HIS A 671 PHE 0.042 0.005 PHE A 657 TYR 0.037 0.005 TYR C 842 ARG 0.018 0.002 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: -0.0326 (ttt) cc_final: -0.2749 (mmt) REVERT: B 786 GLN cc_start: 0.1543 (pm20) cc_final: 0.1080 (pp30) REVERT: C 828 MET cc_start: 0.3121 (mtp) cc_final: 0.2503 (tpt) outliers start: 5 outliers final: 3 residues processed: 124 average time/residue: 0.9958 time to fit residues: 144.0883 Evaluate side-chains 97 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 400 ASN A 427 GLN A 461 HIS A 533 GLN A 826 HIS ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 292 ASN B 380 ASN B 496 ASN B 755 GLN C 211 ASN C 219 GLN C 292 ASN C 400 ASN C 436 GLN C 468 ASN C 496 ASN C 568 ASN ** C 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0423 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17829 Z= 0.166 Angle : 0.563 9.830 24206 Z= 0.309 Chirality : 0.045 0.254 2631 Planarity : 0.004 0.054 3191 Dihedral : 5.374 41.010 2440 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 0.79 % Allowed : 5.42 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.17), residues: 2250 helix: 0.74 (0.28), residues: 361 sheet: -0.43 (0.20), residues: 707 loop : -1.32 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 782 HIS 0.005 0.001 HIS B 461 PHE 0.016 0.001 PHE B 382 TYR 0.016 0.001 TYR B 256 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: -0.0273 (ttt) cc_final: -0.2736 (mmt) REVERT: A 477 LEU cc_start: -0.1105 (OUTLIER) cc_final: -0.1387 (mt) REVERT: B 236 MET cc_start: 0.2169 (OUTLIER) cc_final: 0.0823 (mmm) REVERT: B 786 GLN cc_start: 0.1230 (pm20) cc_final: 0.0993 (pp30) REVERT: C 828 MET cc_start: 0.2496 (mtp) cc_final: 0.2092 (tpt) REVERT: C 874 MET cc_start: 0.1160 (OUTLIER) cc_final: 0.0951 (mtp) outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.9453 time to fit residues: 114.8290 Evaluate side-chains 95 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 874 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 0.0770 chunk 170 optimal weight: 0.0050 chunk 139 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 221 optimal weight: 0.0980 chunk 182 optimal weight: 4.9990 chunk 202 optimal weight: 20.0000 chunk 69 optimal weight: 0.0770 chunk 164 optimal weight: 0.6980 overall best weight: 0.1910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 380 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 687 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0417 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17829 Z= 0.128 Angle : 0.489 7.906 24206 Z= 0.268 Chirality : 0.044 0.173 2631 Planarity : 0.004 0.046 3191 Dihedral : 4.817 25.252 2436 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 0.89 % Allowed : 6.37 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.83 (0.17), residues: 2250 helix: 0.78 (0.27), residues: 382 sheet: -0.25 (0.20), residues: 702 loop : -1.18 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 782 HIS 0.004 0.001 HIS B 352 PHE 0.025 0.001 PHE C 291 TYR 0.009 0.001 TYR B 256 ARG 0.003 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: -0.0103 (ttt) cc_final: -0.2739 (mpt) REVERT: A 855 GLU cc_start: 0.2790 (OUTLIER) cc_final: 0.1898 (mm-30) REVERT: B 236 MET cc_start: 0.2302 (OUTLIER) cc_final: 0.1005 (mmm) REVERT: B 380 ASN cc_start: 0.1349 (OUTLIER) cc_final: 0.0980 (m-40) REVERT: C 828 MET cc_start: 0.2351 (mtp) cc_final: 0.2011 (tpt) REVERT: C 874 MET cc_start: 0.1068 (OUTLIER) cc_final: 0.0665 (mtt) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.8660 time to fit residues: 107.9426 Evaluate side-chains 103 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 874 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.1980 chunk 153 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 0.0070 chunk 97 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 194 optimal weight: 0.2980 chunk 58 optimal weight: 0.4980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 292 ASN B 380 ASN B 834 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0511 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17829 Z= 0.122 Angle : 0.469 7.372 24206 Z= 0.256 Chirality : 0.043 0.156 2631 Planarity : 0.004 0.046 3191 Dihedral : 4.561 25.437 2436 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 1.21 % Allowed : 7.26 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.63 (0.18), residues: 2250 helix: 0.97 (0.27), residues: 380 sheet: -0.20 (0.20), residues: 699 loop : -0.99 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 782 HIS 0.003 0.001 HIS B 461 PHE 0.018 0.001 PHE C 413 TYR 0.011 0.001 TYR C 264 ARG 0.004 0.000 ARG B 850 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: -0.0119 (ttt) cc_final: -0.2386 (ptp) REVERT: A 855 GLU cc_start: 0.2811 (OUTLIER) cc_final: 0.1875 (mm-30) REVERT: B 236 MET cc_start: 0.1858 (OUTLIER) cc_final: 0.0714 (mmm) REVERT: B 380 ASN cc_start: 0.1296 (OUTLIER) cc_final: 0.0964 (m-40) REVERT: C 828 MET cc_start: 0.2217 (mtp) cc_final: 0.1921 (tpt) outliers start: 23 outliers final: 14 residues processed: 103 average time/residue: 0.9187 time to fit residues: 112.3561 Evaluate side-chains 106 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 756 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 341 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN A 873 GLN B 310 ASN B 380 ASN B 431 HIS B 525 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1241 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 17829 Z= 0.358 Angle : 0.804 12.011 24206 Z= 0.441 Chirality : 0.053 0.352 2631 Planarity : 0.006 0.083 3191 Dihedral : 6.064 24.714 2436 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 2.16 % Allowed : 7.57 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.44 (0.17), residues: 2250 helix: 0.54 (0.27), residues: 377 sheet: -0.69 (0.21), residues: 609 loop : -1.59 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 782 HIS 0.014 0.002 HIS B 461 PHE 0.044 0.004 PHE B 430 TYR 0.039 0.003 TYR B 512 ARG 0.013 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 97 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.3496 (m110) cc_final: 0.2635 (m110) REVERT: A 373 MET cc_start: 0.0178 (ttt) cc_final: -0.2261 (ptp) REVERT: A 492 MET cc_start: 0.2740 (tmm) cc_final: 0.2255 (ttt) REVERT: A 855 GLU cc_start: 0.3230 (OUTLIER) cc_final: 0.2209 (mm-30) REVERT: B 441 GLN cc_start: 0.2869 (OUTLIER) cc_final: 0.2653 (mm-40) REVERT: B 518 SER cc_start: 0.1644 (OUTLIER) cc_final: 0.0758 (p) REVERT: C 407 HIS cc_start: 0.0664 (OUTLIER) cc_final: -0.0284 (m90) REVERT: C 441 GLN cc_start: 0.0049 (OUTLIER) cc_final: -0.0853 (mm110) REVERT: C 566 GLU cc_start: 0.3668 (tt0) cc_final: 0.2899 (tt0) REVERT: C 842 TYR cc_start: 0.3597 (m-80) cc_final: 0.3311 (m-80) outliers start: 41 outliers final: 20 residues processed: 123 average time/residue: 0.9777 time to fit residues: 140.3264 Evaluate side-chains 115 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 72 optimal weight: 0.0000 chunk 114 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 341 HIS B 380 ASN B 392 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 672 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 902 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1046 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17829 Z= 0.141 Angle : 0.515 8.348 24206 Z= 0.281 Chirality : 0.044 0.190 2631 Planarity : 0.004 0.052 3191 Dihedral : 5.022 21.610 2436 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 1.58 % Allowed : 9.36 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.17 (0.17), residues: 2250 helix: 0.79 (0.27), residues: 376 sheet: -0.70 (0.21), residues: 648 loop : -1.32 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 782 HIS 0.018 0.001 HIS A 341 PHE 0.019 0.001 PHE B 827 TYR 0.021 0.001 TYR A 540 ARG 0.008 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.2822 (m110) cc_final: 0.2227 (m110) REVERT: A 311 LEU cc_start: 0.2349 (OUTLIER) cc_final: 0.2062 (tp) REVERT: A 373 MET cc_start: -0.0143 (ttt) cc_final: -0.2763 (ptp) REVERT: A 694 MET cc_start: -0.0932 (mmm) cc_final: -0.1201 (ptp) REVERT: A 855 GLU cc_start: 0.3108 (OUTLIER) cc_final: 0.1981 (mm-30) REVERT: B 412 THR cc_start: 0.3337 (OUTLIER) cc_final: 0.3120 (m) REVERT: B 518 SER cc_start: 0.0848 (OUTLIER) cc_final: -0.0022 (p) REVERT: B 874 MET cc_start: 0.3329 (pmm) cc_final: 0.2898 (pmm) REVERT: C 407 HIS cc_start: 0.0677 (OUTLIER) cc_final: -0.1420 (t-170) REVERT: C 566 GLU cc_start: 0.3376 (tt0) cc_final: 0.2549 (tt0) REVERT: C 828 MET cc_start: 0.1729 (mmt) cc_final: 0.1527 (mmt) outliers start: 30 outliers final: 21 residues processed: 108 average time/residue: 0.9853 time to fit residues: 124.7960 Evaluate side-chains 113 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 885 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 216 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 292 ASN A 341 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1134 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17829 Z= 0.165 Angle : 0.519 8.331 24206 Z= 0.283 Chirality : 0.044 0.169 2631 Planarity : 0.004 0.060 3191 Dihedral : 4.924 21.473 2436 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 1.47 % Allowed : 9.42 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.13 (0.17), residues: 2250 helix: 0.85 (0.27), residues: 377 sheet: -0.72 (0.21), residues: 641 loop : -1.27 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 782 HIS 0.008 0.001 HIS A 341 PHE 0.022 0.002 PHE B 382 TYR 0.018 0.001 TYR C 540 ARG 0.004 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.3435 (m110) cc_final: 0.2569 (m110) REVERT: A 373 MET cc_start: -0.0168 (ttt) cc_final: -0.2390 (ptp) REVERT: A 694 MET cc_start: -0.1014 (mmm) cc_final: -0.1470 (ptp) REVERT: A 855 GLU cc_start: 0.3291 (OUTLIER) cc_final: 0.2196 (mm-30) REVERT: B 518 SER cc_start: 0.1117 (OUTLIER) cc_final: 0.0211 (p) REVERT: B 855 GLU cc_start: 0.0660 (OUTLIER) cc_final: -0.0053 (mm-30) REVERT: B 874 MET cc_start: 0.3369 (pmm) cc_final: 0.2923 (pmm) REVERT: C 407 HIS cc_start: 0.0384 (OUTLIER) cc_final: -0.0386 (m90) REVERT: C 566 GLU cc_start: 0.3226 (tt0) cc_final: 0.2468 (tt0) outliers start: 28 outliers final: 18 residues processed: 107 average time/residue: 1.0636 time to fit residues: 132.7303 Evaluate side-chains 107 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 756 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 320 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 407 HIS C 441 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1221 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17829 Z= 0.180 Angle : 0.546 8.691 24206 Z= 0.298 Chirality : 0.045 0.179 2631 Planarity : 0.005 0.061 3191 Dihedral : 5.029 20.603 2436 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 1.84 % Allowed : 9.42 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.14 (0.17), residues: 2250 helix: 0.95 (0.27), residues: 371 sheet: -0.80 (0.21), residues: 625 loop : -1.26 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 782 HIS 0.040 0.002 HIS A 341 PHE 0.026 0.002 PHE B 430 TYR 0.022 0.002 TYR A 540 ARG 0.006 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 89 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LEU cc_start: 0.2456 (OUTLIER) cc_final: 0.2091 (tp) REVERT: A 373 MET cc_start: -0.0039 (ttt) cc_final: -0.2216 (ptp) REVERT: A 855 GLU cc_start: 0.3416 (OUTLIER) cc_final: 0.2204 (mm-30) REVERT: B 234 ASN cc_start: 0.1559 (t0) cc_final: 0.0878 (t0) REVERT: B 518 SER cc_start: 0.1280 (OUTLIER) cc_final: 0.0455 (p) REVERT: B 855 GLU cc_start: 0.0590 (OUTLIER) cc_final: -0.0203 (mm-30) REVERT: C 407 HIS cc_start: 0.0902 (OUTLIER) cc_final: -0.0241 (m90) REVERT: C 566 GLU cc_start: 0.3221 (tt0) cc_final: 0.2326 (tt0) outliers start: 35 outliers final: 25 residues processed: 108 average time/residue: 0.9840 time to fit residues: 124.4105 Evaluate side-chains 116 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 341 HIS A 431 HIS ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 407 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1226 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17829 Z= 0.161 Angle : 0.527 8.709 24206 Z= 0.284 Chirality : 0.044 0.202 2631 Planarity : 0.004 0.061 3191 Dihedral : 4.922 19.222 2436 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 2.00 % Allowed : 9.68 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.11 (0.17), residues: 2250 helix: 1.08 (0.28), residues: 365 sheet: -0.82 (0.21), residues: 630 loop : -1.24 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 782 HIS 0.005 0.001 HIS B 461 PHE 0.023 0.002 PHE B 430 TYR 0.020 0.001 TYR A 540 ARG 0.004 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 91 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LEU cc_start: 0.2477 (OUTLIER) cc_final: 0.2105 (tp) REVERT: A 373 MET cc_start: -0.0404 (ttt) cc_final: -0.2651 (ptp) REVERT: A 855 GLU cc_start: 0.3449 (OUTLIER) cc_final: 0.2194 (mm-30) REVERT: B 518 SER cc_start: 0.1260 (OUTLIER) cc_final: 0.0421 (p) REVERT: B 855 GLU cc_start: 0.0545 (OUTLIER) cc_final: -0.0239 (mm-30) REVERT: B 874 MET cc_start: 0.3617 (pmm) cc_final: 0.3241 (pmm) REVERT: C 407 HIS cc_start: 0.0827 (OUTLIER) cc_final: -0.0985 (t-170) REVERT: C 566 GLU cc_start: 0.3112 (tt0) cc_final: 0.2257 (tt0) REVERT: C 828 MET cc_start: 0.0236 (tpt) cc_final: -0.0003 (mmt) outliers start: 38 outliers final: 27 residues processed: 111 average time/residue: 0.9547 time to fit residues: 124.6476 Evaluate side-chains 121 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.0030 chunk 109 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 407 HIS C 461 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1310 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17829 Z= 0.184 Angle : 0.556 8.900 24206 Z= 0.300 Chirality : 0.045 0.195 2631 Planarity : 0.005 0.066 3191 Dihedral : 5.030 19.434 2436 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 1.95 % Allowed : 9.68 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.22 (0.17), residues: 2250 helix: 1.06 (0.28), residues: 359 sheet: -0.93 (0.20), residues: 647 loop : -1.29 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 782 HIS 0.028 0.001 HIS C 407 PHE 0.030 0.002 PHE B 430 TYR 0.022 0.002 TYR C 540 ARG 0.005 0.001 ARG B 434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LEU cc_start: 0.2514 (OUTLIER) cc_final: 0.2135 (tp) REVERT: A 373 MET cc_start: -0.0038 (ttt) cc_final: -0.2392 (ptp) REVERT: A 855 GLU cc_start: 0.3504 (OUTLIER) cc_final: 0.2020 (mm-30) REVERT: B 279 PHE cc_start: 0.3561 (m-80) cc_final: 0.2722 (m-80) REVERT: B 518 SER cc_start: 0.1373 (OUTLIER) cc_final: 0.0637 (p) REVERT: B 855 GLU cc_start: 0.0816 (OUTLIER) cc_final: 0.0032 (mm-30) REVERT: B 860 VAL cc_start: 0.2229 (p) cc_final: 0.1198 (t) REVERT: B 874 MET cc_start: 0.3671 (pmm) cc_final: 0.3302 (pmm) REVERT: C 407 HIS cc_start: 0.0991 (OUTLIER) cc_final: -0.1878 (t-170) REVERT: C 532 THR cc_start: 0.4595 (p) cc_final: 0.3380 (m) outliers start: 37 outliers final: 24 residues processed: 110 average time/residue: 0.9709 time to fit residues: 125.4613 Evaluate side-chains 120 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 49 optimal weight: 0.0980 chunk 178 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 156 optimal weight: 0.0030 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 407 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5642 r_free = 0.5642 target = 0.412463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5692 r_free = 0.5692 target = 0.403400 restraints weight = 28458.556| |-----------------------------------------------------------------------------| r_work (start): 0.5489 rms_B_bonded: 0.28 r_work: 0.5477 rms_B_bonded: 0.42 restraints_weight: 0.5000 r_work: 0.5459 rms_B_bonded: 0.83 restraints_weight: 0.2500 r_work: 0.5368 rms_B_bonded: 3.42 restraints_weight: 0.1250 r_work (final): 0.5368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1253 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17829 Z= 0.133 Angle : 0.505 8.964 24206 Z= 0.269 Chirality : 0.043 0.152 2631 Planarity : 0.004 0.063 3191 Dihedral : 4.663 19.180 2436 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.42 % Allowed : 10.26 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.02 (0.17), residues: 2250 helix: 1.16 (0.28), residues: 359 sheet: -0.75 (0.20), residues: 643 loop : -1.18 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 782 HIS 0.013 0.001 HIS C 407 PHE 0.015 0.001 PHE A 382 TYR 0.017 0.001 TYR A 540 ARG 0.007 0.000 ARG B 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4488.99 seconds wall clock time: 80 minutes 35.21 seconds (4835.21 seconds total)