Starting phenix.real_space_refine on Thu Sep 18 14:19:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vz3_32219/09_2025/7vz3_32219.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vz3_32219/09_2025/7vz3_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/cci-nas-00/data/ceres_data/7vz3_32219/09_2025/7vz3_32219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vz3_32219/09_2025/7vz3_32219.map" model { file = "/net/cci-nas-00/data/ceres_data/7vz3_32219/09_2025/7vz3_32219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vz3_32219/09_2025/7vz3_32219.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.75, per 1000 atoms: 0.22 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: 1.57 Conformation dependent library (CDL) restraints added in 647.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.67 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: 3.18 Time building geometry restraints manager: 2.08 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: 1.490 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.270 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- 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= 0.419 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.002 ARG A 267 TYR 0.037 0.005 TYR C 842 PHE 0.042 0.005 PHE A 657 TRP 0.106 0.008 TRP C 782 HIS 0.013 0.003 HIS A 671 Details of bonding type rmsd covalent geometry : bond 0.00925 (17829) covalent geometry : angle 1.08333 (24206) hydrogen bonds : bond 0.17073 ( 514) hydrogen bonds : angle 7.11170 ( 1425) *********************** 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 to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.466 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: 0.4454 time to fit residues: 63.5200 Evaluate side-chains 97 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 292 ASN B 341 HIS 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5507 r_free = 0.5507 target = 0.366939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5463 r_free = 0.5463 target = 0.359568 restraints weight = 27389.742| |-----------------------------------------------------------------------------| r_work (start): 0.5469 rms_B_bonded: 1.31 r_work: 0.5433 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.5367 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.5367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0510 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 17829 Z= 0.126 Angle : 0.572 10.357 24206 Z= 0.312 Chirality : 0.045 0.238 2631 Planarity : 0.005 0.055 3191 Dihedral : 5.380 41.039 2440 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.00 % Favored : 95.87 % Rotamer: Outliers : 0.74 % Allowed : 5.79 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.17), residues: 2250 helix: 0.70 (0.28), residues: 361 sheet: -0.45 (0.20), residues: 697 loop : -1.27 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 799 TYR 0.019 0.002 TYR B 256 PHE 0.015 0.002 PHE B 382 TRP 0.030 0.002 TRP B 782 HIS 0.005 0.001 HIS B 461 Details of bonding type rmsd covalent geometry : bond 0.00274 (17829) covalent geometry : angle 0.57221 (24206) hydrogen bonds : bond 0.03676 ( 514) hydrogen bonds : angle 5.45331 ( 1425) *********************** 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 113 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: -0.0038 (ttt) cc_final: -0.2954 (mpt) REVERT: B 236 MET cc_start: 0.2738 (OUTLIER) cc_final: 0.1305 (mmm) REVERT: C 828 MET cc_start: 0.2224 (mtp) cc_final: 0.1529 (tpt) outliers start: 14 outliers final: 5 residues processed: 106 average time/residue: 0.4414 time to fit residues: 54.4055 Evaluate side-chains 95 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 0.0270 chunk 113 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 769 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 380 ASN B 834 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5503 r_free = 0.5503 target = 0.366358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5448 r_free = 0.5448 target = 0.357777 restraints weight = 27237.163| |-----------------------------------------------------------------------------| r_work (start): 0.5452 rms_B_bonded: 1.49 r_work: 0.5412 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.5336 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.5336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0650 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17829 Z= 0.107 Angle : 0.509 7.828 24206 Z= 0.279 Chirality : 0.044 0.195 2631 Planarity : 0.004 0.053 3191 Dihedral : 4.877 25.337 2436 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 1.26 % Allowed : 6.73 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.17), residues: 2250 helix: 0.90 (0.28), residues: 367 sheet: -0.31 (0.20), residues: 664 loop : -1.17 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 850 TYR 0.014 0.001 TYR C 540 PHE 0.026 0.001 PHE C 291 TRP 0.016 0.001 TRP C 782 HIS 0.008 0.001 HIS A 671 Details of bonding type rmsd covalent geometry : bond 0.00235 (17829) covalent geometry : angle 0.50860 (24206) hydrogen bonds : bond 0.03457 ( 514) hydrogen bonds : angle 5.15804 ( 1425) *********************** 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 122 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.0396 (ttt) cc_final: -0.2359 (ptp) REVERT: A 855 GLU cc_start: 0.2742 (OUTLIER) cc_final: 0.1147 (mm-30) REVERT: B 380 ASN cc_start: 0.1782 (OUTLIER) cc_final: 0.1455 (m110) REVERT: B 412 THR cc_start: 0.2419 (OUTLIER) cc_final: 0.2129 (m) REVERT: B 518 SER cc_start: -0.1093 (OUTLIER) cc_final: -0.1906 (p) REVERT: B 660 MET cc_start: 0.0815 (ttt) cc_final: -0.1770 (tmt) REVERT: C 725 MET cc_start: -0.0066 (mpp) cc_final: -0.0308 (tpt) REVERT: C 828 MET cc_start: 0.1932 (mtp) cc_final: 0.1196 (tpt) outliers start: 24 outliers final: 12 residues processed: 115 average time/residue: 0.3790 time to fit residues: 51.8451 Evaluate side-chains 109 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 670 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 380 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 501 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 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 756 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 45 optimal weight: 5.9990 chunk 160 optimal weight: 0.0040 chunk 138 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 206 optimal weight: 0.1980 chunk 109 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.0270 chunk 176 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.3250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN B 392 ASN B 769 GLN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5515 r_free = 0.5515 target = 0.367316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5459 r_free = 0.5459 target = 0.358825 restraints weight = 27059.351| |-----------------------------------------------------------------------------| r_work (start): 0.5465 rms_B_bonded: 1.50 r_work: 0.5423 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.5347 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.5347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0646 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17829 Z= 0.085 Angle : 0.465 7.441 24206 Z= 0.252 Chirality : 0.043 0.185 2631 Planarity : 0.004 0.046 3191 Dihedral : 4.561 25.200 2436 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 1.05 % Allowed : 7.57 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.17), residues: 2250 helix: 1.03 (0.28), residues: 374 sheet: -0.27 (0.20), residues: 672 loop : -1.05 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 401 TYR 0.009 0.001 TYR A 540 PHE 0.018 0.001 PHE B 382 TRP 0.013 0.001 TRP C 782 HIS 0.003 0.001 HIS C 461 Details of bonding type rmsd covalent geometry : bond 0.00182 (17829) covalent geometry : angle 0.46537 (24206) hydrogen bonds : bond 0.02835 ( 514) hydrogen bonds : angle 4.95355 ( 1425) *********************** 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 115 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 MET cc_start: 0.2661 (mmm) cc_final: 0.0095 (mmt) REVERT: A 373 MET cc_start: 0.0517 (ttt) cc_final: -0.2367 (ptp) REVERT: A 492 MET cc_start: 0.0489 (mmt) cc_final: -0.0847 (ttt) REVERT: A 855 GLU cc_start: 0.2715 (OUTLIER) cc_final: 0.1191 (mm-30) REVERT: B 380 ASN cc_start: 0.1508 (OUTLIER) cc_final: 0.1241 (m110) REVERT: C 366 MET cc_start: 0.0231 (tmt) cc_final: -0.0665 (tpp) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.4174 time to fit residues: 51.2983 Evaluate side-chains 109 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN 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 756 THR 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 605 MET Chi-restraints excluded: chain B residue 694 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 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 140 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 902 ASN B 174 GLN B 431 HIS B 525 ASN ** B 834 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 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5642 r_free = 0.5642 target = 0.412825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5700 r_free = 0.5700 target = 0.403765 restraints weight = 28673.959| |-----------------------------------------------------------------------------| r_work (start): 0.5489 rms_B_bonded: 0.33 r_work: 0.5468 rms_B_bonded: 0.52 restraints_weight: 0.5000 r_work: 0.5447 rms_B_bonded: 1.01 restraints_weight: 0.2500 r_work: 0.5330 rms_B_bonded: 4.21 restraints_weight: 0.1250 r_work (final): 0.5330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1187 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17829 Z= 0.166 Angle : 0.651 11.016 24206 Z= 0.354 Chirality : 0.048 0.286 2631 Planarity : 0.005 0.068 3191 Dihedral : 5.421 24.631 2436 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 2.05 % Allowed : 7.89 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.17), residues: 2250 helix: 0.77 (0.27), residues: 376 sheet: -0.72 (0.21), residues: 645 loop : -1.40 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 644 TYR 0.028 0.002 TYR A 540 PHE 0.036 0.003 PHE B 430 TRP 0.014 0.002 TRP B 782 HIS 0.011 0.002 HIS C 461 Details of bonding type rmsd covalent geometry : bond 0.00358 (17829) covalent geometry : angle 0.65114 (24206) hydrogen bonds : bond 0.03776 ( 514) hydrogen bonds : angle 5.68707 ( 1425) *********************** 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 131 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.3268 (m110) cc_final: 0.2142 (m110) REVERT: A 366 MET cc_start: 0.2357 (mmm) cc_final: 0.0201 (mmm) REVERT: A 373 MET cc_start: 0.0691 (ttt) cc_final: -0.2385 (ptp) REVERT: A 492 MET cc_start: 0.0902 (mmt) cc_final: -0.0778 (mmt) REVERT: A 855 GLU cc_start: 0.3425 (OUTLIER) cc_final: 0.1669 (mm-30) REVERT: B 412 THR cc_start: 0.3065 (OUTLIER) cc_final: 0.2778 (m) REVERT: B 441 GLN cc_start: 0.3056 (OUTLIER) cc_final: 0.2765 (mm110) REVERT: B 518 SER cc_start: 0.1009 (OUTLIER) cc_final: 0.0085 (p) REVERT: C 407 HIS cc_start: 0.0848 (OUTLIER) cc_final: -0.0313 (m90) REVERT: C 566 GLU cc_start: 0.3563 (tt0) cc_final: 0.2623 (tt0) REVERT: C 874 MET cc_start: 0.0512 (mtt) cc_final: 0.0191 (mtp) outliers start: 39 outliers final: 24 residues processed: 116 average time/residue: 0.4508 time to fit residues: 60.8548 Evaluate side-chains 113 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN 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 412 THR Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 605 MET 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 441 GLN Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 725 MET 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 176 optimal weight: 5.9990 chunk 132 optimal weight: 0.0370 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN B 310 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS C 407 HIS C 461 HIS C 672 ASN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5635 r_free = 0.5635 target = 0.412225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5694 r_free = 0.5694 target = 0.403246 restraints weight = 28566.770| |-----------------------------------------------------------------------------| r_work (start): 0.5482 rms_B_bonded: 0.32 r_work: 0.5465 rms_B_bonded: 0.51 restraints_weight: 0.5000 r_work: 0.5444 rms_B_bonded: 1.01 restraints_weight: 0.2500 r_work: 0.5332 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.5332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1497 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17829 Z= 0.191 Angle : 0.691 10.790 24206 Z= 0.381 Chirality : 0.049 0.195 2631 Planarity : 0.006 0.061 3191 Dihedral : 5.888 21.823 2436 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 2.31 % Allowed : 9.00 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2250 helix: 0.38 (0.27), residues: 378 sheet: -1.12 (0.20), residues: 647 loop : -1.64 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 850 TYR 0.034 0.002 TYR A 540 PHE 0.045 0.003 PHE B 430 TRP 0.029 0.002 TRP C 627 HIS 0.009 0.002 HIS B 461 Details of bonding type rmsd covalent geometry : bond 0.00416 (17829) covalent geometry : angle 0.69146 (24206) hydrogen bonds : bond 0.04101 ( 514) hydrogen bonds : angle 6.05444 ( 1425) *********************** 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 146 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LEU cc_start: 0.2619 (OUTLIER) cc_final: 0.2067 (tp) REVERT: A 366 MET cc_start: 0.2532 (mmm) cc_final: 0.0503 (mmm) REVERT: A 373 MET cc_start: 0.0662 (ttt) cc_final: -0.2355 (ptp) REVERT: A 492 MET cc_start: 0.0840 (mmt) cc_final: -0.0980 (mmt) REVERT: A 660 MET cc_start: 0.2598 (mmp) cc_final: 0.2369 (mmp) REVERT: A 692 ARG cc_start: 0.3514 (OUTLIER) cc_final: 0.1504 (mpp-170) REVERT: A 855 GLU cc_start: 0.3920 (OUTLIER) cc_final: 0.1952 (mm-30) REVERT: B 441 GLN cc_start: 0.3105 (OUTLIER) cc_final: 0.2670 (mm-40) REVERT: B 842 TYR cc_start: 0.3892 (m-80) cc_final: 0.2083 (m-80) REVERT: B 847 ASP cc_start: 0.1350 (OUTLIER) cc_final: 0.1030 (m-30) REVERT: B 855 GLU cc_start: 0.1017 (OUTLIER) cc_final: 0.0040 (mm-30) REVERT: B 874 MET cc_start: 0.3663 (pmm) cc_final: 0.3294 (pmm) REVERT: C 274 PHE cc_start: 0.1767 (p90) cc_final: 0.1194 (m-80) REVERT: C 407 HIS cc_start: 0.1254 (OUTLIER) cc_final: -0.1168 (t-170) outliers start: 44 outliers final: 24 residues processed: 129 average time/residue: 0.4168 time to fit residues: 63.2319 Evaluate side-chains 124 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 847 ASP 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 407 HIS Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 734 SER 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 94 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 46 optimal weight: 0.0050 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 162 optimal weight: 0.0870 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 625 ASN B 769 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.366049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5447 r_free = 0.5447 target = 0.357851 restraints weight = 26707.362| |-----------------------------------------------------------------------------| r_work (start): 0.5439 rms_B_bonded: 1.46 r_work: 0.5399 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.5318 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.5318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1408 moved from start: 0.5130 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= 0.115 Angle : 0.539 9.076 24206 Z= 0.295 Chirality : 0.045 0.257 2631 Planarity : 0.004 0.062 3191 Dihedral : 5.263 20.861 2436 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 2.05 % Allowed : 9.84 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.17), residues: 2250 helix: 0.65 (0.27), residues: 377 sheet: -1.04 (0.20), residues: 649 loop : -1.50 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 434 TYR 0.026 0.001 TYR A 540 PHE 0.026 0.002 PHE B 430 TRP 0.015 0.001 TRP C 782 HIS 0.007 0.001 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00249 (17829) covalent geometry : angle 0.53915 (24206) hydrogen bonds : bond 0.03179 ( 514) hydrogen bonds : angle 5.61387 ( 1425) *********************** 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 133 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.0069 (ttt) cc_final: -0.2583 (ptp) REVERT: A 492 MET cc_start: 0.0801 (mmt) cc_final: -0.0970 (mmt) REVERT: A 855 GLU cc_start: 0.3951 (OUTLIER) cc_final: 0.1634 (mm-30) REVERT: B 279 PHE cc_start: 0.3635 (m-80) cc_final: 0.3192 (m-80) REVERT: B 518 SER cc_start: 0.1783 (OUTLIER) cc_final: 0.0882 (p) REVERT: B 842 TYR cc_start: 0.3732 (m-80) cc_final: 0.3289 (m-80) REVERT: B 860 VAL cc_start: 0.2672 (p) cc_final: 0.1455 (t) REVERT: B 874 MET cc_start: 0.3420 (pmm) cc_final: 0.3089 (pmm) REVERT: B 905 MET cc_start: 0.4624 (mmm) cc_final: 0.4301 (mmp) REVERT: C 366 MET cc_start: 0.1285 (tmt) cc_final: 0.0138 (tpt) REVERT: C 407 HIS cc_start: 0.1457 (OUTLIER) cc_final: -0.0843 (t-170) outliers start: 39 outliers final: 28 residues processed: 117 average time/residue: 0.4178 time to fit residues: 57.3840 Evaluate side-chains 122 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 611 TYR 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 A residue 874 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 277 GLU 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 605 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 828 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 319 LEU Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 700 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 183 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5498 r_free = 0.5498 target = 0.365824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5446 r_free = 0.5446 target = 0.357575 restraints weight = 26611.875| |-----------------------------------------------------------------------------| r_work (start): 0.5439 rms_B_bonded: 1.46 r_work: 0.5398 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.5321 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.5321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1424 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17829 Z= 0.114 Angle : 0.546 14.454 24206 Z= 0.294 Chirality : 0.045 0.193 2631 Planarity : 0.004 0.063 3191 Dihedral : 5.095 22.746 2436 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 2.16 % Allowed : 9.78 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.17), residues: 2250 helix: 0.84 (0.28), residues: 364 sheet: -0.99 (0.20), residues: 650 loop : -1.44 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 434 TYR 0.022 0.001 TYR A 540 PHE 0.025 0.002 PHE B 430 TRP 0.014 0.001 TRP C 782 HIS 0.007 0.001 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00249 (17829) covalent geometry : angle 0.54562 (24206) hydrogen bonds : bond 0.03110 ( 514) hydrogen bonds : angle 5.52909 ( 1425) *********************** 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 137 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.0164 (ttt) cc_final: -0.2521 (ptp) REVERT: A 492 MET cc_start: 0.0879 (mmt) cc_final: -0.0902 (mmt) REVERT: A 855 GLU cc_start: 0.3995 (OUTLIER) cc_final: 0.1662 (mm-30) REVERT: B 234 ASN cc_start: 0.0803 (t0) cc_final: 0.0518 (t0) REVERT: B 412 THR cc_start: 0.3034 (p) cc_final: 0.2722 (m) REVERT: B 518 SER cc_start: 0.1737 (OUTLIER) cc_final: 0.0899 (p) REVERT: B 847 ASP cc_start: 0.1391 (OUTLIER) cc_final: 0.1074 (m-30) REVERT: B 860 VAL cc_start: 0.2887 (p) cc_final: 0.1765 (t) REVERT: B 905 MET cc_start: 0.4378 (mmm) cc_final: 0.4124 (mmp) REVERT: C 407 HIS cc_start: 0.1249 (OUTLIER) cc_final: -0.0925 (t-170) outliers start: 41 outliers final: 32 residues processed: 122 average time/residue: 0.4266 time to fit residues: 60.9176 Evaluate side-chains 130 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 641 ILE 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 A residue 874 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 277 GLU 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 605 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 847 ASP 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 466 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 794 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 93 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS C 630 ASN C 769 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5496 r_free = 0.5496 target = 0.365691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5442 r_free = 0.5442 target = 0.357425 restraints weight = 26547.396| |-----------------------------------------------------------------------------| r_work (start): 0.5434 rms_B_bonded: 1.46 r_work: 0.5397 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.5321 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.5321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1483 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17829 Z= 0.118 Angle : 0.545 12.883 24206 Z= 0.294 Chirality : 0.044 0.168 2631 Planarity : 0.004 0.066 3191 Dihedral : 5.027 20.196 2436 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 2.31 % Allowed : 9.63 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.17), residues: 2250 helix: 0.89 (0.28), residues: 359 sheet: -1.00 (0.20), residues: 633 loop : -1.43 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 850 TYR 0.022 0.001 TYR A 540 PHE 0.027 0.002 PHE B 430 TRP 0.014 0.001 TRP C 782 HIS 0.024 0.001 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00260 (17829) covalent geometry : angle 0.54484 (24206) hydrogen bonds : bond 0.03131 ( 514) hydrogen bonds : angle 5.54433 ( 1425) *********************** 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 136 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 MET cc_start: 0.1519 (mmm) cc_final: 0.0625 (mtt) REVERT: A 373 MET cc_start: 0.0251 (ttt) cc_final: -0.2781 (ptp) REVERT: A 492 MET cc_start: 0.0959 (mmt) cc_final: -0.0864 (mmt) REVERT: A 855 GLU cc_start: 0.3976 (OUTLIER) cc_final: 0.1734 (mm-30) REVERT: B 412 THR cc_start: 0.2989 (p) cc_final: 0.2701 (m) REVERT: B 847 ASP cc_start: 0.1236 (OUTLIER) cc_final: 0.0847 (t0) REVERT: B 860 VAL cc_start: 0.3367 (p) cc_final: 0.2350 (t) REVERT: C 366 MET cc_start: 0.0746 (tmt) cc_final: -0.0273 (tpp) REVERT: C 407 HIS cc_start: 0.1191 (OUTLIER) cc_final: -0.1878 (t-170) REVERT: C 828 MET cc_start: 0.3713 (mmt) cc_final: 0.3224 (mmt) outliers start: 44 outliers final: 37 residues processed: 118 average time/residue: 0.4558 time to fit residues: 62.4449 Evaluate side-chains 130 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 425 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 605 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 847 ASP 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 466 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 794 ILE 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 77 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN A 676 GLN A 718 HIS ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 352 HIS ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 407 HIS C 441 GLN C 533 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5466 r_free = 0.5466 target = 0.361937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5409 r_free = 0.5409 target = 0.353106 restraints weight = 26136.033| |-----------------------------------------------------------------------------| r_work (start): 0.5415 rms_B_bonded: 1.50 r_work: 0.5376 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.5295 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.5295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1823 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17829 Z= 0.205 Angle : 0.726 12.699 24206 Z= 0.396 Chirality : 0.050 0.221 2631 Planarity : 0.006 0.085 3191 Dihedral : 6.036 26.562 2436 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 2.42 % Allowed : 9.89 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2250 helix: 0.42 (0.27), residues: 360 sheet: -1.31 (0.20), residues: 629 loop : -1.80 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 524 TYR 0.035 0.003 TYR A 540 PHE 0.058 0.003 PHE B 430 TRP 0.025 0.002 TRP B 782 HIS 0.057 0.003 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00457 (17829) covalent geometry : angle 0.72588 (24206) hydrogen bonds : bond 0.04276 ( 514) hydrogen bonds : angle 6.39372 ( 1425) ********************** 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 141 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.0904 (mmt) cc_final: -0.0979 (mmt) REVERT: A 605 MET cc_start: 0.2593 (pmm) cc_final: -0.0738 (tpt) REVERT: A 692 ARG cc_start: 0.4046 (OUTLIER) cc_final: 0.3477 (mmp80) REVERT: A 828 MET cc_start: 0.1276 (mtp) cc_final: 0.0822 (mtm) REVERT: A 855 GLU cc_start: 0.3771 (OUTLIER) cc_final: 0.1668 (mm-30) REVERT: B 847 ASP cc_start: 0.1660 (OUTLIER) cc_final: 0.0959 (m-30) REVERT: B 905 MET cc_start: 0.4735 (mmm) cc_final: 0.4450 (mmp) REVERT: C 274 PHE cc_start: 0.2159 (p90) cc_final: 0.0943 (p90) REVERT: C 366 MET cc_start: 0.1253 (tmt) cc_final: 0.0006 (tpp) REVERT: C 407 HIS cc_start: 0.1591 (OUTLIER) cc_final: -0.1832 (t-170) REVERT: C 441 GLN cc_start: 0.0766 (OUTLIER) cc_final: 0.0223 (mm-40) REVERT: C 512 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.2941 (t80) outliers start: 46 outliers final: 30 residues processed: 124 average time/residue: 0.4515 time to fit residues: 65.4656 Evaluate side-chains 126 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 460 VAL 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 605 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 847 ASP Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 284 THR 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 466 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 794 ILE 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 219 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 207 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 902 ASN ** 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 = 0.5470 r_free = 0.5470 target = 0.362913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5415 r_free = 0.5415 target = 0.353987 restraints weight = 26049.130| |-----------------------------------------------------------------------------| r_work (start): 0.5419 rms_B_bonded: 1.55 r_work: 0.5374 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.5290 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.5290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1812 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 17829 Z= 0.205 Angle : 0.902 59.151 24206 Z= 0.507 Chirality : 0.049 0.380 2631 Planarity : 0.006 0.084 3191 Dihedral : 6.017 26.495 2436 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.96 % Rotamer: Outliers : 2.21 % Allowed : 10.57 % Favored : 87.22 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.17), residues: 2250 helix: 0.40 (0.27), residues: 360 sheet: -1.33 (0.20), residues: 629 loop : -1.82 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 644 TYR 0.031 0.002 TYR A 540 PHE 0.053 0.003 PHE B 430 TRP 0.020 0.002 TRP B 782 HIS 0.043 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00444 (17829) covalent geometry : angle 0.90192 (24206) hydrogen bonds : bond 0.04221 ( 514) hydrogen bonds : angle 6.38579 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6612.80 seconds wall clock time: 113 minutes 24.20 seconds (6804.20 seconds total)