Starting phenix.real_space_refine on Sun Jun 15 13:52:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vz3_32219/06_2025/7vz3_32219.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vz3_32219/06_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_32219/06_2025/7vz3_32219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vz3_32219/06_2025/7vz3_32219.map" model { file = "/net/cci-nas-00/data/ceres_data/7vz3_32219/06_2025/7vz3_32219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vz3_32219/06_2025/7vz3_32219.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10985 2.51 5 N 2950 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17415 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5798 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 720} Chain: "B" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5819 Classifications: {'peptide': 754} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 723} Chain: "C" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5798 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 720} Time building chain proxies: 10.83, per 1000 atoms: 0.62 Number of scatterers: 17415 At special positions: 0 Unit cell: (94.569, 93.482, 192.399, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3414 8.00 N 2950 7.00 C 10985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 2.5 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 24 sheets defined 20.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 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: 8.46 Time building geometry restraints manager: 5.13 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: 0.010 Normalize map: mean=0, sd=1: 77.080 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 45.230 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2250 helix: -0.07 (0.27), residues: 374 sheet: -0.52 (0.20), residues: 699 loop : -1.51 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.008 TRP C 782 HIS 0.013 0.003 HIS A 671 PHE 0.042 0.005 PHE A 657 TYR 0.037 0.005 TYR C 842 ARG 0.018 0.002 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.17073 ( 514) hydrogen bonds : angle 7.11170 ( 1425) covalent geometry : bond 0.00925 (17829) covalent geometry : angle 1.08333 (24206) *********************** 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 : 1.636 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: 1.0846 time to fit residues: 157.0611 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 : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 400 ASN A 427 GLN A 461 HIS A 533 GLN A 826 HIS ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 292 ASN B 380 ASN B 496 ASN B 755 GLN C 211 ASN C 219 GLN C 292 ASN C 400 ASN C 436 GLN C 468 ASN C 496 ASN C 568 ASN ** C 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5500 r_free = 0.5500 target = 0.366438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5456 r_free = 0.5456 target = 0.358746 restraints weight = 27613.579| |-----------------------------------------------------------------------------| r_work (start): 0.5468 rms_B_bonded: 1.35 r_work: 0.5429 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.5360 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.5360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0437 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17829 Z= 0.121 Angle : 0.563 9.830 24206 Z= 0.309 Chirality : 0.045 0.254 2631 Planarity : 0.004 0.054 3191 Dihedral : 5.374 41.010 2440 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 0.79 % Allowed : 5.42 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2250 helix: 0.74 (0.28), residues: 361 sheet: -0.43 (0.20), residues: 707 loop : -1.32 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 782 HIS 0.005 0.001 HIS B 461 PHE 0.016 0.001 PHE B 382 TYR 0.016 0.001 TYR B 256 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 514) hydrogen bonds : angle 5.49166 ( 1425) covalent geometry : bond 0.00253 (17829) covalent geometry : angle 0.56322 (24206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: -0.0030 (ttt) cc_final: -0.2765 (mmt) REVERT: A 477 LEU cc_start: -0.1303 (OUTLIER) cc_final: -0.1568 (mt) REVERT: B 236 MET cc_start: 0.2291 (OUTLIER) cc_final: 0.0902 (mmm) REVERT: C 828 MET cc_start: 0.2186 (mtp) cc_final: 0.1456 (tpt) outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.9847 time to fit residues: 118.9665 Evaluate side-chains 93 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 892 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 182 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 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 769 GLN B 292 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN B 431 HIS B 525 ASN B 834 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 520 HIS ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5495 r_free = 0.5495 target = 0.364113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5427 r_free = 0.5427 target = 0.354892 restraints weight = 26470.633| |-----------------------------------------------------------------------------| r_work (start): 0.5429 rms_B_bonded: 1.58 r_work: 0.5387 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.5301 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.5301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1408 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 17829 Z= 0.284 Angle : 0.920 12.894 24206 Z= 0.506 Chirality : 0.057 0.326 2631 Planarity : 0.008 0.074 3191 Dihedral : 6.875 26.977 2436 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer: Outliers : 2.26 % Allowed : 7.31 % Favored : 90.43 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2250 helix: 0.18 (0.27), residues: 368 sheet: -0.83 (0.21), residues: 603 loop : -1.89 (0.15), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 695 HIS 0.018 0.003 HIS B 642 PHE 0.054 0.004 PHE C 291 TYR 0.046 0.004 TYR C 540 ARG 0.014 0.002 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.05942 ( 514) hydrogen bonds : angle 6.64344 ( 1425) covalent geometry : bond 0.00630 (17829) covalent geometry : angle 0.92000 (24206) *********************** 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 151 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.3759 (m110) cc_final: 0.2697 (m110) REVERT: A 302 THR cc_start: 0.2569 (m) cc_final: 0.2350 (m) REVERT: A 373 MET cc_start: 0.0742 (ttt) cc_final: -0.2380 (ptp) REVERT: A 855 GLU cc_start: 0.3631 (OUTLIER) cc_final: 0.1598 (mm-30) REVERT: B 441 GLN cc_start: 0.3417 (OUTLIER) cc_final: 0.3042 (mm110) REVERT: B 518 SER cc_start: 0.2255 (OUTLIER) cc_final: 0.1403 (p) REVERT: B 799 ARG cc_start: 0.3481 (ptm160) cc_final: 0.1594 (ptm160) REVERT: C 366 MET cc_start: 0.0505 (tmt) cc_final: -0.0439 (tpp) REVERT: C 407 HIS cc_start: 0.0877 (OUTLIER) cc_final: 0.0055 (m90) REVERT: C 566 GLU cc_start: 0.3214 (tt0) cc_final: 0.2549 (tt0) REVERT: C 828 MET cc_start: 0.2153 (mtp) cc_final: 0.1446 (mmt) outliers start: 43 outliers final: 18 residues processed: 137 average time/residue: 0.9854 time to fit residues: 158.1949 Evaluate side-chains 117 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 892 ILE 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 587 LYS Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 212 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 214 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 150 optimal weight: 0.2980 chunk 158 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 452 GLN A 713 ASN ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 292 ASN B 341 HIS ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 672 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5642 r_free = 0.5642 target = 0.412738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5700 r_free = 0.5700 target = 0.403726 restraints weight = 28593.425| |-----------------------------------------------------------------------------| r_work (start): 0.5493 rms_B_bonded: 0.34 r_work: 0.5475 rms_B_bonded: 0.52 restraints_weight: 0.5000 r_work: 0.5454 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.5343 rms_B_bonded: 4.24 restraints_weight: 0.1250 r_work (final): 0.5343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1171 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17829 Z= 0.115 Angle : 0.551 7.959 24206 Z= 0.302 Chirality : 0.045 0.174 2631 Planarity : 0.004 0.056 3191 Dihedral : 5.483 22.876 2436 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 1.58 % Allowed : 8.68 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2250 helix: 0.63 (0.27), residues: 374 sheet: -0.79 (0.21), residues: 638 loop : -1.55 (0.15), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 782 HIS 0.005 0.001 HIS C 461 PHE 0.016 0.001 PHE C 797 TYR 0.022 0.001 TYR A 540 ARG 0.003 0.000 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 514) hydrogen bonds : angle 5.65044 ( 1425) covalent geometry : bond 0.00247 (17829) covalent geometry : angle 0.55067 (24206) *********************** 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 123 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.2986 (m110) cc_final: 0.2052 (m110) REVERT: A 373 MET cc_start: 0.0227 (ttt) cc_final: -0.2784 (ptp) REVERT: A 492 MET cc_start: 0.2132 (tmm) cc_final: 0.1697 (ttt) REVERT: A 855 GLU cc_start: 0.3878 (OUTLIER) cc_final: 0.1816 (mm-30) REVERT: B 860 VAL cc_start: 0.3046 (p) cc_final: 0.1670 (t) REVERT: C 407 HIS cc_start: 0.0995 (OUTLIER) cc_final: -0.1256 (t-170) REVERT: C 566 GLU cc_start: 0.3054 (tt0) cc_final: 0.2224 (tt0) REVERT: C 842 TYR cc_start: 0.3436 (m-80) cc_final: 0.3027 (m-80) outliers start: 30 outliers final: 19 residues processed: 116 average time/residue: 0.9862 time to fit residues: 134.3222 Evaluate side-chains 110 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 256 TYR Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 654 SER 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 466 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 734 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 201 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 214 optimal weight: 0.5980 chunk 182 optimal weight: 9.9990 chunk 32 optimal weight: 0.0470 chunk 163 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 902 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5641 r_free = 0.5641 target = 0.412771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5697 r_free = 0.5697 target = 0.404002 restraints weight = 28960.560| |-----------------------------------------------------------------------------| r_work (start): 0.5495 rms_B_bonded: 0.30 r_work: 0.5478 rms_B_bonded: 0.47 restraints_weight: 0.5000 r_work: 0.5458 rms_B_bonded: 0.94 restraints_weight: 0.2500 r_work: 0.5354 rms_B_bonded: 3.92 restraints_weight: 0.1250 r_work (final): 0.5354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1218 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17829 Z= 0.106 Angle : 0.517 7.392 24206 Z= 0.284 Chirality : 0.044 0.207 2631 Planarity : 0.004 0.055 3191 Dihedral : 5.138 22.997 2436 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 2.31 % Allowed : 9.21 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2250 helix: 0.74 (0.27), residues: 374 sheet: -0.76 (0.21), residues: 640 loop : -1.46 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 782 HIS 0.004 0.001 HIS A 671 PHE 0.017 0.001 PHE B 382 TYR 0.017 0.001 TYR A 540 ARG 0.006 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 514) hydrogen bonds : angle 5.42495 ( 1425) covalent geometry : bond 0.00230 (17829) covalent geometry : angle 0.51734 (24206) *********************** 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 132 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ASN cc_start: 0.3422 (m110) cc_final: 0.1767 (m110) REVERT: A 373 MET cc_start: 0.0284 (ttt) cc_final: -0.2709 (ptp) REVERT: A 492 MET cc_start: 0.2424 (tmm) cc_final: 0.1927 (ttt) REVERT: A 855 GLU cc_start: 0.3888 (OUTLIER) cc_final: 0.1886 (mm-30) REVERT: B 518 SER cc_start: 0.1883 (OUTLIER) cc_final: 0.0902 (p) REVERT: B 855 GLU cc_start: 0.0872 (OUTLIER) cc_final: -0.0115 (mm-30) REVERT: B 860 VAL cc_start: 0.3137 (p) cc_final: 0.1868 (t) REVERT: C 366 MET cc_start: -0.0075 (tmt) cc_final: -0.0680 (tpp) REVERT: C 405 LEU cc_start: 0.1600 (OUTLIER) cc_final: 0.1207 (mt) REVERT: C 407 HIS cc_start: 0.0573 (OUTLIER) cc_final: -0.1619 (t-170) REVERT: C 566 GLU cc_start: 0.2953 (tt0) cc_final: 0.2096 (tt0) REVERT: C 842 TYR cc_start: 0.3562 (m-80) cc_final: 0.3156 (m-80) outliers start: 44 outliers final: 29 residues processed: 119 average time/residue: 0.9533 time to fit residues: 133.1798 Evaluate side-chains 120 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 LEU 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 B residue 256 TYR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 401 ARG 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 654 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 786 GLN 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 284 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 794 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 158 optimal weight: 0.0570 chunk 179 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 89 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 2 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5499 r_free = 0.5499 target = 0.365487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5447 r_free = 0.5447 target = 0.357512 restraints weight = 26892.679| |-----------------------------------------------------------------------------| r_work (start): 0.5439 rms_B_bonded: 1.45 r_work: 0.5397 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.5316 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.5316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1539 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17829 Z= 0.167 Angle : 0.644 8.252 24206 Z= 0.355 Chirality : 0.047 0.256 2631 Planarity : 0.006 0.073 3191 Dihedral : 5.707 22.069 2436 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 3.31 % Allowed : 9.42 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2250 helix: 0.62 (0.28), residues: 364 sheet: -1.07 (0.21), residues: 628 loop : -1.62 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 782 HIS 0.008 0.002 HIS B 461 PHE 0.043 0.003 PHE B 430 TYR 0.029 0.002 TYR A 540 ARG 0.007 0.001 ARG B 434 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 514) hydrogen bonds : angle 5.79440 ( 1425) covalent geometry : bond 0.00362 (17829) covalent geometry : angle 0.64383 (24206) *********************** 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 162 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 99 time to evaluate : 1.662 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: 0.0907 (ttt) cc_final: -0.2337 (ptp) REVERT: A 694 MET cc_start: -0.0480 (mmm) cc_final: -0.1043 (ptp) REVERT: A 855 GLU cc_start: 0.3948 (OUTLIER) cc_final: 0.1809 (mm-30) REVERT: B 498 VAL cc_start: -0.2825 (OUTLIER) cc_final: -0.3117 (p) REVERT: B 855 GLU cc_start: 0.1462 (OUTLIER) cc_final: 0.0413 (mm-30) REVERT: B 874 MET cc_start: 0.3766 (pmm) cc_final: 0.3479 (pmm) REVERT: C 274 PHE cc_start: 0.1603 (p90) cc_final: 0.1070 (m-80) REVERT: C 366 MET cc_start: 0.0550 (tmt) cc_final: -0.0293 (tpp) REVERT: C 407 HIS cc_start: 0.1149 (OUTLIER) cc_final: 0.0267 (m90) REVERT: C 532 THR cc_start: 0.4637 (p) cc_final: 0.3041 (m) REVERT: C 545 GLU cc_start: 0.4255 (OUTLIER) cc_final: 0.3981 (pt0) REVERT: C 842 TYR cc_start: 0.3730 (m-80) cc_final: 0.3238 (m-80) outliers start: 63 outliers final: 43 residues processed: 144 average time/residue: 1.0691 time to fit residues: 181.1837 Evaluate side-chains 139 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 652 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 B residue 242 GLU Chi-restraints excluded: chain B residue 256 TYR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 498 VAL 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 599 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 786 GLN 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 270 ASN Chi-restraints excluded: chain C residue 277 GLU 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 466 ILE Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 122 optimal weight: 0.0470 chunk 165 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 168 optimal weight: 0.1980 chunk 118 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 HIS ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 516 GLN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5642 r_free = 0.5642 target = 0.412697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5701 r_free = 0.5701 target = 0.403874 restraints weight = 28880.061| |-----------------------------------------------------------------------------| r_work (start): 0.5484 rms_B_bonded: 0.29 r_work: 0.5468 rms_B_bonded: 0.45 restraints_weight: 0.5000 r_work: 0.5449 rms_B_bonded: 0.88 restraints_weight: 0.2500 r_work: 0.5341 rms_B_bonded: 3.77 restraints_weight: 0.1250 r_work (final): 0.5341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1380 moved from start: 0.5095 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= 0.100 Angle : 0.521 10.537 24206 Z= 0.284 Chirality : 0.044 0.159 2631 Planarity : 0.004 0.065 3191 Dihedral : 5.102 19.891 2436 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 2.16 % Allowed : 10.94 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2250 helix: 0.88 (0.28), residues: 364 sheet: -1.00 (0.21), residues: 638 loop : -1.45 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 782 HIS 0.005 0.001 HIS C 407 PHE 0.019 0.001 PHE C 274 TYR 0.022 0.001 TYR A 540 ARG 0.003 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 514) hydrogen bonds : angle 5.46568 ( 1425) covalent geometry : bond 0.00217 (17829) covalent geometry : angle 0.52072 (24206) *********************** 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 132 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.0703 (ttt) cc_final: -0.2344 (ptp) REVERT: A 492 MET cc_start: 0.2371 (tmm) cc_final: 0.1565 (ttm) REVERT: A 694 MET cc_start: -0.0930 (mmm) cc_final: -0.1333 (ptp) REVERT: A 855 GLU cc_start: 0.3904 (OUTLIER) cc_final: 0.1841 (mm-30) REVERT: B 498 VAL cc_start: -0.2659 (OUTLIER) cc_final: -0.2934 (p) REVERT: B 874 MET cc_start: 0.3978 (pmm) cc_final: 0.3732 (pmm) REVERT: C 177 GLN cc_start: 0.5762 (tm130) cc_final: 0.4891 (pm20) REVERT: C 366 MET cc_start: 0.0552 (tmt) cc_final: -0.0031 (tpp) REVERT: C 407 HIS cc_start: 0.0940 (OUTLIER) cc_final: -0.0090 (m90) REVERT: C 842 TYR cc_start: 0.3752 (m-80) cc_final: 0.3157 (m-80) outliers start: 41 outliers final: 29 residues processed: 118 average time/residue: 0.9201 time to fit residues: 127.6117 Evaluate side-chains 119 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 611 TYR 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 277 GLU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 498 VAL 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 654 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 786 GLN 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 466 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 130 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 51 optimal weight: 0.0570 chunk 172 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 112 optimal weight: 0.1980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 HIS ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN B 625 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS C 769 GLN C 834 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5643 r_free = 0.5643 target = 0.412730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5699 r_free = 0.5699 target = 0.403979 restraints weight = 28556.081| |-----------------------------------------------------------------------------| r_work (start): 0.5486 rms_B_bonded: 0.28 r_work: 0.5471 rms_B_bonded: 0.42 restraints_weight: 0.5000 r_work: 0.5454 rms_B_bonded: 0.82 restraints_weight: 0.2500 r_work: 0.5352 rms_B_bonded: 3.51 restraints_weight: 0.1250 r_work (final): 0.5352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1333 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17829 Z= 0.091 Angle : 0.488 7.208 24206 Z= 0.268 Chirality : 0.043 0.152 2631 Planarity : 0.004 0.063 3191 Dihedral : 4.738 19.938 2436 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 2.10 % Allowed : 11.20 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2250 helix: 1.01 (0.28), residues: 370 sheet: -0.87 (0.20), residues: 660 loop : -1.39 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 782 HIS 0.017 0.001 HIS A 671 PHE 0.016 0.001 PHE C 413 TYR 0.016 0.001 TYR A 540 ARG 0.002 0.000 ARG B 434 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 514) hydrogen bonds : angle 5.26025 ( 1425) covalent geometry : bond 0.00197 (17829) covalent geometry : angle 0.48769 (24206) *********************** 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 130 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.0773 (ttt) cc_final: -0.2326 (ptp) REVERT: A 492 MET cc_start: 0.2312 (tmm) cc_final: 0.1546 (ttt) REVERT: A 694 MET cc_start: -0.0941 (mmm) cc_final: -0.1299 (ptp) REVERT: A 855 GLU cc_start: 0.4056 (OUTLIER) cc_final: 0.1740 (mm-30) REVERT: B 234 ASN cc_start: 0.0658 (t0) cc_final: 0.0350 (t0) REVERT: B 498 VAL cc_start: -0.2379 (OUTLIER) cc_final: -0.2660 (p) REVERT: B 874 MET cc_start: 0.3865 (pmm) cc_final: 0.3630 (pmm) REVERT: C 366 MET cc_start: 0.0397 (tmt) cc_final: -0.0266 (tpt) REVERT: C 407 HIS cc_start: 0.0673 (OUTLIER) cc_final: -0.0175 (m90) REVERT: C 566 GLU cc_start: 0.3578 (tt0) cc_final: 0.2476 (tt0) REVERT: C 842 TYR cc_start: 0.3680 (m-80) cc_final: 0.3147 (m-80) outliers start: 40 outliers final: 31 residues processed: 116 average time/residue: 1.2311 time to fit residues: 170.9256 Evaluate side-chains 124 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR 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 538 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 637 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 256 TYR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain C residue 236 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 587 LYS Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 905 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 154 optimal weight: 30.0000 chunk 91 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN C 630 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5494 r_free = 0.5494 target = 0.364933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5439 r_free = 0.5439 target = 0.356650 restraints weight = 26609.287| |-----------------------------------------------------------------------------| r_work (start): 0.5429 rms_B_bonded: 1.49 r_work: 0.5388 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.5307 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.5307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1688 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17829 Z= 0.170 Angle : 0.645 8.754 24206 Z= 0.353 Chirality : 0.047 0.176 2631 Planarity : 0.006 0.083 3191 Dihedral : 5.568 22.703 2436 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 2.37 % Allowed : 11.36 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2250 helix: 0.77 (0.28), residues: 358 sheet: -0.98 (0.21), residues: 617 loop : -1.68 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 782 HIS 0.040 0.002 HIS A 671 PHE 0.045 0.003 PHE B 430 TYR 0.028 0.002 TYR A 540 ARG 0.008 0.001 ARG B 434 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 514) hydrogen bonds : angle 5.87224 ( 1425) covalent geometry : bond 0.00372 (17829) covalent geometry : angle 0.64534 (24206) *********************** 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 134 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 MET cc_start: 0.2590 (mmp) cc_final: 0.1814 (mmp) REVERT: A 694 MET cc_start: -0.0538 (mmm) cc_final: -0.1119 (ptp) REVERT: A 855 GLU cc_start: 0.4175 (OUTLIER) cc_final: 0.1900 (mm-30) REVERT: B 460 VAL cc_start: 0.1042 (OUTLIER) cc_final: 0.0436 (t) REVERT: B 498 VAL cc_start: -0.2761 (OUTLIER) cc_final: -0.3102 (p) REVERT: C 366 MET cc_start: 0.0959 (tmt) cc_final: 0.0009 (tpp) REVERT: C 407 HIS cc_start: 0.1076 (OUTLIER) cc_final: 0.0509 (m90) REVERT: C 441 GLN cc_start: 0.0219 (OUTLIER) cc_final: -0.1022 (mm-40) REVERT: C 512 TYR cc_start: 0.3843 (OUTLIER) cc_final: 0.3014 (t80) REVERT: C 725 MET cc_start: 0.0190 (pmm) cc_final: -0.1241 (tpt) REVERT: C 842 TYR cc_start: 0.3926 (m-80) cc_final: 0.3284 (m-80) outliers start: 45 outliers final: 31 residues processed: 122 average time/residue: 1.1590 time to fit residues: 167.5133 Evaluate side-chains 124 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 2.024 ------------------------------------------------------------------------------- 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 535 ASN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 256 TYR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 498 VAL 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 599 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 277 GLU 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 512 TYR Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 644 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 756 THR 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 130 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.365189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.356724 restraints weight = 26524.458| |-----------------------------------------------------------------------------| r_work (start): 0.5430 rms_B_bonded: 1.51 r_work: 0.5389 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.5306 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.5306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1689 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 17829 Z= 0.179 Angle : 0.799 59.197 24206 Z= 0.461 Chirality : 0.047 0.175 2631 Planarity : 0.005 0.080 3191 Dihedral : 5.554 22.645 2436 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 2.16 % Allowed : 11.94 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.17), residues: 2250 helix: 0.75 (0.28), residues: 358 sheet: -1.00 (0.21), residues: 617 loop : -1.71 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 782 HIS 0.032 0.002 HIS A 671 PHE 0.043 0.003 PHE B 430 TYR 0.027 0.002 TYR C 540 ARG 0.009 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 514) hydrogen bonds : angle 5.86877 ( 1425) covalent geometry : bond 0.00400 (17829) covalent geometry : angle 0.79869 (24206) ********************** 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 127 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 MET cc_start: 0.2501 (mmp) cc_final: 0.1738 (mmp) REVERT: A 694 MET cc_start: -0.0578 (mmm) cc_final: -0.1105 (ptp) REVERT: A 855 GLU cc_start: 0.4130 (OUTLIER) cc_final: 0.1928 (mm-30) REVERT: B 460 VAL cc_start: 0.1002 (OUTLIER) cc_final: 0.0385 (t) REVERT: B 498 VAL cc_start: -0.2770 (OUTLIER) cc_final: -0.3107 (p) REVERT: C 366 MET cc_start: 0.0951 (tmt) cc_final: 0.0025 (tpp) REVERT: C 407 HIS cc_start: 0.1042 (OUTLIER) cc_final: 0.0491 (m90) REVERT: C 512 TYR cc_start: 0.3857 (OUTLIER) cc_final: 0.3043 (t80) REVERT: C 842 TYR cc_start: 0.3897 (m-80) cc_final: 0.3281 (m-80) outliers start: 41 outliers final: 34 residues processed: 116 average time/residue: 1.1007 time to fit residues: 148.6335 Evaluate side-chains 125 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 538 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 671 HIS Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain B residue 256 TYR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 498 VAL 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 599 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 644 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 756 THR 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 220 optimal weight: 0.3980 chunk 174 optimal weight: 0.0970 chunk 192 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 140 optimal weight: 0.2980 chunk 210 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5497 r_free = 0.5497 target = 0.365222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.356688 restraints weight = 26580.014| |-----------------------------------------------------------------------------| r_work (start): 0.5429 rms_B_bonded: 1.53 r_work: 0.5387 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.5306 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.5306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1685 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 17829 Z= 0.179 Angle : 0.799 59.197 24206 Z= 0.461 Chirality : 0.047 0.175 2631 Planarity : 0.005 0.080 3191 Dihedral : 5.554 22.645 2436 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 2.05 % Allowed : 12.05 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.17), residues: 2250 helix: 0.75 (0.28), residues: 358 sheet: -1.00 (0.21), residues: 617 loop : -1.71 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 782 HIS 0.032 0.002 HIS A 671 PHE 0.043 0.003 PHE B 430 TYR 0.027 0.002 TYR C 540 ARG 0.009 0.001 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 514) hydrogen bonds : angle 5.86877 ( 1425) covalent geometry : bond 0.00400 (17829) covalent geometry : angle 0.79869 (24206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15458.38 seconds wall clock time: 273 minutes 13.89 seconds (16393.89 seconds total)