Starting phenix.real_space_refine on Fri Sep 27 17:31:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/09_2024/7vyv_32215.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/09_2024/7vyv_32215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/09_2024/7vyv_32215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/09_2024/7vyv_32215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/09_2024/7vyv_32215.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/09_2024/7vyv_32215.cif" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10572 2.51 5 N 2817 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16698 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5566 Classifications: {'peptide': 720} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689} Chain: "B" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5566 Classifications: {'peptide': 720} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689} Chain: "C" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5566 Classifications: {'peptide': 720} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689} Time building chain proxies: 8.94, per 1000 atoms: 0.54 Number of scatterers: 16698 At special positions: 0 Unit cell: (93.482, 92.395, 180.442, 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 3243 8.00 N 2817 7.00 C 10572 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: 3.53 Conformation dependent library (CDL) restraints added in 1.9 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 17.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 186 through 192 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 187 through 192 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 659 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 828 through 832 Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 886 through 902 Processing helix chain 'C' and resid 187 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 354 through 357 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 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 886 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 225 removed outlier: 5.674A pdb=" N SER A 225 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY A 239 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.498A pdb=" N PHE A 274 " --> pdb=" O ASN A 320 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 318 through 320 current: chain 'A' and resid 375 through 382 removed outlier: 7.150A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 428 through 431 current: chain 'A' and resid 640 through 641 Processing sheet with id=AA3, first strand: chain 'A' and resid 334 through 336 removed outlier: 6.428A pdb=" N LEU A 334 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 364 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 392 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET A 366 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 389 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR A 418 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 391 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY A 442 " --> pdb=" O TRP A 415 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN A 441 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN A 501 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY A 499 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 528 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 530 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 503 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 532 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN A 505 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA A 577 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 601 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AA5, first strand: chain 'A' and resid 795 through 801 removed outlier: 3.744A pdb=" N TYR A 751 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 757 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE A 838 " --> pdb=" O THR A 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 671 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 843 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU A 669 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR A 845 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 667 " --> pdb=" O TYR A 845 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 732 removed outlier: 3.972A pdb=" N LEU A 727 " --> pdb=" O PHE A 813 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.445A pdb=" N ILE B 841 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN B 672 " --> pdb=" O LEU B 839 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 839 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 838 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR B 757 " --> pdb=" O PHE B 838 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 225 removed outlier: 5.659A pdb=" N SER B 225 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 239 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.392A pdb=" N PHE B 274 " --> pdb=" O ASN B 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AB4, first strand: chain 'B' and resid 727 through 732 removed outlier: 3.974A pdb=" N LEU B 727 " --> pdb=" O PHE B 813 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 858 through 859 removed outlier: 6.393A pdb=" N ILE C 841 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 672 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 839 " --> pdb=" O ASN C 672 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE C 838 " --> pdb=" O THR C 757 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR C 757 " --> pdb=" O PHE C 838 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 751 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 220 through 225 removed outlier: 5.570A pdb=" N SER C 225 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY C 239 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 263 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.519A pdb=" N PHE C 274 " --> pdb=" O ASN C 320 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 318 through 320 current: chain 'C' and resid 375 through 382 removed outlier: 7.069A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 405 " --> pdb=" O HIS C 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 428 through 431 current: chain 'C' and resid 640 through 641 Processing sheet with id=AB8, first strand: chain 'C' and resid 334 through 336 removed outlier: 6.493A pdb=" N LEU C 334 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA C 364 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASN C 392 " --> pdb=" O ALA C 364 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET C 366 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE C 417 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C 392 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 419 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP C 415 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE C 444 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE C 417 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU C 446 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL C 419 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN C 441 " --> pdb=" O GLY C 499 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN C 501 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS C 500 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU C 528 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA C 577 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER C 527 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 579 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 529 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N SER C 581 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 531 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 601 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TRP C 627 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 602 " --> pdb=" O TRP C 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 480 through 482 Processing sheet with id=AC1, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AC2, first strand: chain 'C' and resid 727 through 732 removed outlier: 3.916A pdb=" N LEU C 727 " --> pdb=" O PHE C 813 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 966 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: 4.92 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4700 1.33 - 1.47: 5221 1.47 - 1.60: 7086 1.60 - 1.74: 1 1.74 - 1.87: 104 Bond restraints: 17112 Sorted by residual: bond pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " ideal model delta sigma weight residual 1.520 1.419 0.101 3.00e-02 1.11e+03 1.14e+01 bond pdb=" C LEU A 212 " pdb=" N LYS A 213 " ideal model delta sigma weight residual 1.328 1.273 0.055 1.67e-02 3.59e+03 1.08e+01 bond pdb=" CG GLN A 755 " pdb=" CD GLN A 755 " ideal model delta sigma weight residual 1.516 1.595 -0.079 2.50e-02 1.60e+03 1.00e+01 bond pdb=" CG LEU B 311 " pdb=" CD1 LEU B 311 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.57e+00 bond pdb=" CG LEU C 311 " pdb=" CD1 LEU C 311 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.08e+00 ... (remaining 17107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 21602 1.95 - 3.89: 1350 3.89 - 5.84: 222 5.84 - 7.79: 53 7.79 - 9.74: 11 Bond angle restraints: 23238 Sorted by residual: angle pdb=" N LYS A 750 " pdb=" CA LYS A 750 " pdb=" C LYS A 750 " ideal model delta sigma weight residual 112.12 120.32 -8.20 1.34e+00 5.57e-01 3.74e+01 angle pdb=" N ILE B 693 " pdb=" CA ILE B 693 " pdb=" C ILE B 693 " ideal model delta sigma weight residual 110.62 116.49 -5.87 1.02e+00 9.61e-01 3.31e+01 angle pdb=" N ILE A 693 " pdb=" CA ILE A 693 " pdb=" C ILE A 693 " ideal model delta sigma weight residual 110.62 116.47 -5.85 1.02e+00 9.61e-01 3.29e+01 angle pdb=" N GLU A 748 " pdb=" CA GLU A 748 " pdb=" C GLU A 748 " ideal model delta sigma weight residual 111.36 117.34 -5.98 1.09e+00 8.42e-01 3.01e+01 angle pdb=" N GLU C 748 " pdb=" CA GLU C 748 " pdb=" C GLU C 748 " ideal model delta sigma weight residual 111.36 117.33 -5.97 1.09e+00 8.42e-01 3.00e+01 ... (remaining 23233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9243 17.95 - 35.90: 609 35.90 - 53.84: 85 53.84 - 71.79: 16 71.79 - 89.74: 22 Dihedral angle restraints: 9975 sinusoidal: 3783 harmonic: 6192 Sorted by residual: 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 -150.28 -29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ASP B 847 " pdb=" C ASP B 847 " pdb=" N LEU B 848 " pdb=" CA LEU B 848 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASN C 400 " pdb=" C ASN C 400 " pdb=" N ARG C 401 " pdb=" CA ARG C 401 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 9972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2013 0.081 - 0.163: 455 0.163 - 0.244: 43 0.244 - 0.325: 6 0.325 - 0.407: 3 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA VAL A 885 " pdb=" N VAL A 885 " pdb=" C VAL A 885 " pdb=" CB VAL A 885 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.13e+00 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 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA VAL C 885 " pdb=" N VAL C 885 " pdb=" C VAL C 885 " pdb=" CB VAL C 885 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2517 not shown) Planarity restraints: 3051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 782 " 0.095 2.00e-02 2.50e+03 6.74e-02 1.13e+02 pdb=" CG TRP B 782 " -0.167 2.00e-02 2.50e+03 pdb=" CD1 TRP B 782 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP B 782 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP B 782 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 782 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 782 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 782 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 782 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 782 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 782 " -0.078 2.00e-02 2.50e+03 5.92e-02 8.77e+01 pdb=" CG TRP C 782 " 0.153 2.00e-02 2.50e+03 pdb=" CD1 TRP C 782 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP C 782 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP C 782 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 782 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 782 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 782 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 782 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 782 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 782 " 0.080 2.00e-02 2.50e+03 5.92e-02 8.76e+01 pdb=" CG TRP A 782 " -0.152 2.00e-02 2.50e+03 pdb=" CD1 TRP A 782 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP A 782 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 782 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 782 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 782 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 782 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 782 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 782 " 0.015 2.00e-02 2.50e+03 ... (remaining 3048 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2883 2.77 - 3.30: 15318 3.30 - 3.83: 28079 3.83 - 4.37: 36520 4.37 - 4.90: 61142 Nonbonded interactions: 143942 Sorted by model distance: nonbonded pdb=" NH1 ARG B 395 " pdb=" O GLU B 423 " model vdw 2.235 3.120 nonbonded pdb=" NH1 ARG A 395 " pdb=" O GLU A 423 " model vdw 2.274 3.120 nonbonded pdb=" O PHE B 291 " pdb=" O ASN B 384 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP C 572 " pdb=" OG SER C 574 " model vdw 2.295 3.040 nonbonded pdb=" O PHE A 291 " pdb=" O ASN A 384 " model vdw 2.324 3.040 ... (remaining 143937 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.110 Set scattering table: 0.130 Process input model: 34.520 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 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 0.101 17112 Z= 0.609 Angle : 1.098 9.735 23238 Z= 0.638 Chirality : 0.068 0.407 2520 Planarity : 0.007 0.067 3051 Dihedral : 13.116 89.740 6045 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.15 % 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: 2154 helix: -0.99 (0.28), residues: 303 sheet: -0.22 (0.21), residues: 639 loop : -1.30 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.167 0.010 TRP B 782 HIS 0.012 0.003 HIS C 461 PHE 0.042 0.005 PHE B 382 TYR 0.027 0.004 TYR A 842 ARG 0.009 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.933 Fit side-chains REVERT: A 305 MET cc_start: 0.9226 (tpp) cc_final: 0.8839 (tpp) REVERT: A 453 GLU cc_start: 0.7802 (pm20) cc_final: 0.7383 (pm20) REVERT: B 563 ASP cc_start: 0.8068 (m-30) cc_final: 0.7805 (m-30) REVERT: B 700 MET cc_start: 0.9342 (mmm) cc_final: 0.9077 (mmm) REVERT: C 236 MET cc_start: 0.9186 (mmm) cc_final: 0.8844 (mmm) REVERT: C 660 MET cc_start: 0.9143 (ttt) cc_final: 0.8698 (ttt) REVERT: C 902 ASN cc_start: 0.8611 (m-40) cc_final: 0.8307 (m110) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 1.5671 time to fit residues: 300.3534 Evaluate side-chains 129 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 356 ASN A 400 ASN A 509 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS A 889 ASN A 902 ASN B 193 GLN B 292 ASN B 384 ASN B 400 ASN B 427 GLN B 431 HIS B 456 HIS B 464 ASN B 509 ASN B 744 ASN B 755 GLN B 826 HIS B 873 GLN B 889 ASN C 211 ASN C 219 GLN C 292 ASN C 501 GLN C 607 ASN C 625 ASN C 744 ASN C 873 GLN C 902 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17112 Z= 0.209 Angle : 0.602 7.089 23238 Z= 0.336 Chirality : 0.048 0.156 2520 Planarity : 0.005 0.045 3051 Dihedral : 5.594 24.435 2337 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 0.99 % Allowed : 5.76 % Favored : 93.26 % 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: -1.07 (0.17), residues: 2154 helix: -0.16 (0.29), residues: 303 sheet: -0.12 (0.20), residues: 675 loop : -1.20 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP C 782 HIS 0.004 0.001 HIS C 461 PHE 0.018 0.002 PHE C 382 TYR 0.018 0.002 TYR A 256 ARG 0.006 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.887 Fit side-chains REVERT: A 453 GLU cc_start: 0.7771 (pm20) cc_final: 0.7405 (pm20) REVERT: A 548 ASN cc_start: 0.8824 (t0) cc_final: 0.8525 (t0) REVERT: A 902 ASN cc_start: 0.8298 (m110) cc_final: 0.7544 (m110) REVERT: B 198 ASP cc_start: 0.8515 (t0) cc_final: 0.8070 (t0) REVERT: B 700 MET cc_start: 0.9298 (mmm) cc_final: 0.9018 (mmm) REVERT: B 855 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: B 905 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5487 (mtt) REVERT: C 236 MET cc_start: 0.9200 (mmm) cc_final: 0.8927 (mmm) REVERT: C 660 MET cc_start: 0.9038 (ttt) cc_final: 0.8665 (ttt) outliers start: 18 outliers final: 4 residues processed: 154 average time/residue: 1.4624 time to fit residues: 248.8453 Evaluate side-chains 138 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain B residue 905 MET Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 486 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN B 292 ASN B 367 ASN B 392 ASN B 456 HIS C 219 GLN C 292 ASN C 431 HIS C 902 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17112 Z= 0.222 Angle : 0.589 7.443 23238 Z= 0.328 Chirality : 0.048 0.157 2520 Planarity : 0.005 0.043 3051 Dihedral : 5.434 23.708 2337 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 1.21 % Allowed : 7.24 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2154 helix: 0.05 (0.30), residues: 303 sheet: -0.09 (0.20), residues: 675 loop : -1.14 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 782 HIS 0.004 0.001 HIS C 826 PHE 0.021 0.002 PHE B 382 TYR 0.015 0.002 TYR C 609 ARG 0.006 0.001 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.955 Fit side-chains REVERT: A 548 ASN cc_start: 0.8768 (t0) cc_final: 0.8456 (t0) REVERT: A 694 MET cc_start: 0.8996 (mmm) cc_final: 0.8590 (mtp) REVERT: A 902 ASN cc_start: 0.8235 (m110) cc_final: 0.7512 (m110) REVERT: B 198 ASP cc_start: 0.8492 (t0) cc_final: 0.8060 (t0) REVERT: B 700 MET cc_start: 0.9246 (mmm) cc_final: 0.8989 (mmm) REVERT: B 855 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: C 198 ASP cc_start: 0.8467 (t0) cc_final: 0.8157 (t0) REVERT: C 660 MET cc_start: 0.8994 (ttt) cc_final: 0.8597 (ttt) outliers start: 22 outliers final: 6 residues processed: 154 average time/residue: 1.4734 time to fit residues: 250.5842 Evaluate side-chains 139 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 367 ASN A 392 ASN A 760 ASN A 873 GLN B 292 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17112 Z= 0.405 Angle : 0.719 8.566 23238 Z= 0.402 Chirality : 0.054 0.188 2520 Planarity : 0.006 0.047 3051 Dihedral : 5.828 25.809 2337 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.83 % Favored : 95.03 % Rotamer: Outliers : 1.21 % Allowed : 8.44 % Favored : 90.35 % 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: -1.12 (0.17), residues: 2154 helix: -0.23 (0.29), residues: 303 sheet: -0.19 (0.20), residues: 675 loop : -1.19 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 782 HIS 0.007 0.002 HIS C 826 PHE 0.031 0.002 PHE B 382 TYR 0.021 0.003 TYR C 609 ARG 0.007 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.992 Fit side-chains REVERT: A 548 ASN cc_start: 0.8855 (t0) cc_final: 0.8545 (t0) REVERT: A 694 MET cc_start: 0.9068 (mmm) cc_final: 0.8568 (mtp) REVERT: A 902 ASN cc_start: 0.8245 (m110) cc_final: 0.7586 (m110) REVERT: B 198 ASP cc_start: 0.8506 (t0) cc_final: 0.8078 (t0) REVERT: B 700 MET cc_start: 0.9160 (mmm) cc_final: 0.8849 (mmm) REVERT: B 855 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: C 660 MET cc_start: 0.9013 (ttt) cc_final: 0.8608 (ttt) outliers start: 22 outliers final: 8 residues processed: 148 average time/residue: 1.4077 time to fit residues: 231.2430 Evaluate side-chains 138 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 760 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 873 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17112 Z= 0.289 Angle : 0.640 8.477 23238 Z= 0.356 Chirality : 0.050 0.162 2520 Planarity : 0.005 0.047 3051 Dihedral : 5.673 25.277 2337 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 1.21 % Allowed : 9.16 % Favored : 89.64 % 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: -1.10 (0.17), residues: 2154 helix: -0.17 (0.29), residues: 303 sheet: -0.21 (0.20), residues: 675 loop : -1.17 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 782 HIS 0.005 0.001 HIS C 826 PHE 0.026 0.002 PHE B 382 TYR 0.016 0.002 TYR C 609 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.928 Fit side-chains REVERT: A 548 ASN cc_start: 0.8789 (t0) cc_final: 0.8475 (t0) REVERT: A 694 MET cc_start: 0.9082 (mmm) cc_final: 0.8630 (mtp) REVERT: A 864 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8564 (ttm170) REVERT: A 902 ASN cc_start: 0.8243 (m110) cc_final: 0.7569 (m110) REVERT: B 198 ASP cc_start: 0.8492 (t0) cc_final: 0.8093 (t0) REVERT: B 855 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: C 492 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8977 (ptp) outliers start: 22 outliers final: 7 residues processed: 149 average time/residue: 1.3893 time to fit residues: 229.6010 Evaluate side-chains 143 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 760 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 873 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17112 Z= 0.270 Angle : 0.626 8.333 23238 Z= 0.348 Chirality : 0.049 0.158 2520 Planarity : 0.005 0.046 3051 Dihedral : 5.609 25.081 2337 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.83 % Favored : 95.03 % Rotamer: Outliers : 1.64 % Allowed : 8.99 % Favored : 89.36 % 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: -1.08 (0.17), residues: 2154 helix: -0.12 (0.30), residues: 303 sheet: -0.20 (0.20), residues: 675 loop : -1.17 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 782 HIS 0.005 0.001 HIS C 826 PHE 0.025 0.002 PHE B 382 TYR 0.016 0.002 TYR C 609 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.916 Fit side-chains REVERT: A 548 ASN cc_start: 0.8753 (t0) cc_final: 0.8433 (t0) REVERT: A 694 MET cc_start: 0.9095 (mmm) cc_final: 0.8679 (mtp) REVERT: A 864 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8424 (ttm170) REVERT: A 902 ASN cc_start: 0.8231 (m110) cc_final: 0.7567 (m110) REVERT: B 198 ASP cc_start: 0.8490 (t0) cc_final: 0.8145 (t0) REVERT: B 855 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: C 492 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8973 (ptp) outliers start: 30 outliers final: 12 residues processed: 152 average time/residue: 1.3147 time to fit residues: 222.5178 Evaluate side-chains 146 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN B 219 GLN B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 873 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17112 Z= 0.247 Angle : 0.606 8.173 23238 Z= 0.337 Chirality : 0.048 0.156 2520 Planarity : 0.005 0.044 3051 Dihedral : 5.544 25.025 2337 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.54 % Rotamer: Outliers : 1.54 % Allowed : 9.38 % Favored : 89.09 % 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: -1.04 (0.17), residues: 2154 helix: -0.08 (0.30), residues: 303 sheet: -0.18 (0.20), residues: 675 loop : -1.14 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 695 HIS 0.004 0.001 HIS B 456 PHE 0.024 0.002 PHE B 382 TYR 0.015 0.002 TYR C 609 ARG 0.006 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.845 Fit side-chains REVERT: A 548 ASN cc_start: 0.8726 (t0) cc_final: 0.8402 (t0) REVERT: A 694 MET cc_start: 0.9087 (mmm) cc_final: 0.8671 (mtp) REVERT: A 864 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8424 (ttm170) REVERT: A 902 ASN cc_start: 0.8216 (m110) cc_final: 0.7554 (m110) REVERT: B 198 ASP cc_start: 0.8487 (t0) cc_final: 0.8074 (t0) REVERT: B 599 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8813 (tt) REVERT: B 855 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: C 486 ASN cc_start: 0.8944 (m-40) cc_final: 0.8734 (m110) REVERT: C 492 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8961 (ptp) outliers start: 28 outliers final: 13 residues processed: 156 average time/residue: 1.2983 time to fit residues: 226.4113 Evaluate side-chains 153 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 0.0030 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 873 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17112 Z= 0.194 Angle : 0.563 7.824 23238 Z= 0.313 Chirality : 0.047 0.149 2520 Planarity : 0.004 0.043 3051 Dihedral : 5.366 24.270 2337 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 1.54 % Allowed : 9.38 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2154 helix: -0.04 (0.30), residues: 303 sheet: -0.17 (0.20), residues: 696 loop : -1.15 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 695 HIS 0.004 0.001 HIS B 456 PHE 0.021 0.001 PHE B 382 TYR 0.012 0.001 TYR C 609 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.993 Fit side-chains REVERT: A 548 ASN cc_start: 0.8661 (t0) cc_final: 0.8331 (t0) REVERT: A 694 MET cc_start: 0.9076 (mmm) cc_final: 0.8678 (mtp) REVERT: A 864 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8414 (ttm170) REVERT: A 902 ASN cc_start: 0.8194 (m110) cc_final: 0.7532 (m110) REVERT: B 198 ASP cc_start: 0.8481 (t0) cc_final: 0.8067 (t0) REVERT: B 599 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8840 (tt) REVERT: B 855 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: C 492 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8960 (ptp) outliers start: 28 outliers final: 10 residues processed: 159 average time/residue: 1.3463 time to fit residues: 239.4140 Evaluate side-chains 145 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 760 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17112 Z= 0.305 Angle : 0.647 8.249 23238 Z= 0.360 Chirality : 0.050 0.161 2520 Planarity : 0.005 0.044 3051 Dihedral : 5.603 25.183 2337 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.74 % Favored : 95.13 % Rotamer: Outliers : 1.21 % Allowed : 9.81 % Favored : 88.98 % 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: -1.06 (0.17), residues: 2154 helix: -0.15 (0.30), residues: 303 sheet: -0.19 (0.20), residues: 675 loop : -1.14 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 695 HIS 0.005 0.001 HIS B 456 PHE 0.026 0.002 PHE B 382 TYR 0.017 0.002 TYR C 609 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.868 Fit side-chains REVERT: A 548 ASN cc_start: 0.8739 (t0) cc_final: 0.8412 (t0) REVERT: A 694 MET cc_start: 0.9101 (mmm) cc_final: 0.8661 (mtp) REVERT: A 902 ASN cc_start: 0.8245 (m110) cc_final: 0.7585 (m110) REVERT: B 198 ASP cc_start: 0.8497 (t0) cc_final: 0.8145 (t0) REVERT: B 375 ARG cc_start: 0.8229 (mtm180) cc_final: 0.7895 (ttm-80) REVERT: B 599 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8817 (tt) REVERT: B 855 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: C 486 ASN cc_start: 0.8950 (m-40) cc_final: 0.8723 (m110) REVERT: C 492 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8973 (ptp) outliers start: 22 outliers final: 12 residues processed: 155 average time/residue: 1.3186 time to fit residues: 227.7958 Evaluate side-chains 152 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 456 HIS Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 902 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17112 Z= 0.162 Angle : 0.540 7.697 23238 Z= 0.299 Chirality : 0.046 0.145 2520 Planarity : 0.004 0.043 3051 Dihedral : 5.311 24.148 2337 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Rotamer: Outliers : 0.93 % Allowed : 10.25 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2154 helix: 0.02 (0.30), residues: 303 sheet: -0.15 (0.20), residues: 696 loop : -1.13 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 415 HIS 0.025 0.001 HIS C 456 PHE 0.018 0.001 PHE B 382 TYR 0.014 0.001 TYR A 256 ARG 0.003 0.000 ARG A 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 2.073 Fit side-chains REVERT: A 548 ASN cc_start: 0.8631 (t0) cc_final: 0.8296 (t0) REVERT: A 694 MET cc_start: 0.9075 (mmm) cc_final: 0.8681 (mtp) REVERT: A 902 ASN cc_start: 0.8171 (m110) cc_final: 0.7512 (m110) REVERT: B 198 ASP cc_start: 0.8473 (t0) cc_final: 0.8067 (t0) REVERT: B 599 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8833 (tt) REVERT: B 855 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: C 492 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8961 (ptp) outliers start: 17 outliers final: 8 residues processed: 150 average time/residue: 1.4197 time to fit residues: 236.2468 Evaluate side-chains 146 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 171 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.074385 restraints weight = 19798.061| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.29 r_work: 0.2681 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17112 Z= 0.150 Angle : 0.516 7.449 23238 Z= 0.286 Chirality : 0.045 0.140 2520 Planarity : 0.004 0.042 3051 Dihedral : 5.079 22.795 2337 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.46 % Favored : 95.40 % Rotamer: Outliers : 0.99 % Allowed : 10.25 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2154 helix: 0.13 (0.31), residues: 303 sheet: -0.09 (0.20), residues: 696 loop : -1.07 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 265 HIS 0.005 0.001 HIS C 456 PHE 0.017 0.001 PHE B 382 TYR 0.012 0.001 TYR A 256 ARG 0.003 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5029.09 seconds wall clock time: 89 minutes 41.25 seconds (5381.25 seconds total)