Starting phenix.real_space_refine on Wed Aug 5 14:59:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2026/8sea_40408.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 37 5.16 5 C 6490 2.51 5 N 1792 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7712 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 926} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLY%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.17 Number of scatterers: 10208 At special positions: 0 Unit cell: (91.652, 104.983, 117.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 1 15.00 O 1888 8.00 N 1792 7.00 C 6490 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 225.3 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 44.9% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.059A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.527A pdb=" N ALA A 74 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.077A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.031A pdb=" N HIS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.517A pdb=" N ASN A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 266 through 273 removed outlier: 4.330A pdb=" N LEU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 415 through 423 removed outlier: 4.640A pdb=" N VAL A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 442 through 455 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.128A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.951A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.522A pdb=" N VAL A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.554A pdb=" N ARG A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.306A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 607 through 631 removed outlier: 3.870A pdb=" N LEU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.554A pdb=" N HIS A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 removed outlier: 4.000A pdb=" N THR A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.518A pdb=" N LEU A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'A' and resid 761 through 765 removed outlier: 4.070A pdb=" N MET A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.914A pdb=" N GLN A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.557A pdb=" N SER A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 873 Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.511A pdb=" N LEU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.701A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.873A pdb=" N VAL C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.726A pdb=" N LEU D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 Processing helix chain 'D' and resid 136 through 141 removed outlier: 4.430A pdb=" N TYR D 140 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.301A pdb=" N VAL A 35 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.301A pdb=" N VAL A 35 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179 removed outlier: 4.492A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.739A pdb=" N LEU A 236 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.083A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL A 535 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA A 562 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA A 537 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 919 removed outlier: 6.502A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 98 removed outlier: 9.051A pdb=" N VAL B 148 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 85 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N MET B 150 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG B 87 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU B 152 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.029A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.029A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 149 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 124 through 126 removed outlier: 3.508A pdb=" N THR D 125 " --> pdb=" O PHE D 149 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1281 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: 1.43 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3420 1.34 - 1.46: 1327 1.46 - 1.57: 5653 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 10460 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.415 1.624 -0.209 1.50e-02 4.44e+03 1.94e+02 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.526 1.366 0.160 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.454 1.295 0.159 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.497 -0.142 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 14137 2.71 - 5.41: 94 5.41 - 8.12: 6 8.12 - 10.82: 1 10.82 - 13.53: 4 Bond angle restraints: 14242 Sorted by residual: angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 114.00 127.43 -13.43 1.50e+00 4.44e-01 8.02e+01 angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 108.20 95.38 12.82 1.50e+00 4.44e-01 7.30e+01 angle pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C4' AMP B1101 " ideal model delta sigma weight residual 109.70 104.33 5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.37 13.53 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C3' AMP B1101 " ideal model delta sigma weight residual 101.50 105.75 -4.25 1.00e+00 1.00e+00 1.81e+01 ... (remaining 14237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 5680 13.84 - 27.68: 436 27.68 - 41.52: 142 41.52 - 55.36: 27 55.36 - 69.21: 14 Dihedral angle restraints: 6299 sinusoidal: 2548 harmonic: 3751 Sorted by residual: dihedral pdb=" C1' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C5' AMP B1101 " ideal model delta sinusoidal sigma weight residual -123.00 -152.80 29.80 1 8.00e+00 1.56e-02 1.98e+01 dihedral pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" CB PHE A 211 " pdb=" CG PHE A 211 " ideal model delta sinusoidal sigma weight residual -60.00 -0.14 -59.86 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 895 " pdb=" CB ARG A 895 " pdb=" CG ARG A 895 " pdb=" CD ARG A 895 " ideal model delta sinusoidal sigma weight residual -60.00 -118.15 58.15 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 979 0.028 - 0.057: 427 0.057 - 0.085: 98 0.085 - 0.114: 75 0.114 - 0.142: 12 Chirality restraints: 1591 Sorted by residual: chirality pdb=" CA GLN A 385 " pdb=" N GLN A 385 " pdb=" C GLN A 385 " pdb=" CB GLN A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE A 834 " pdb=" N ILE A 834 " pdb=" C ILE A 834 " pdb=" CB ILE A 834 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1588 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 76 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO C 77 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 77 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 77 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 876 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 877 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 877 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 877 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 759 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO A 760 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.014 5.00e-02 4.00e+02 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 2 2.00 - 2.72: 415 2.72 - 3.45: 14994 3.45 - 4.17: 23096 4.17 - 4.90: 42039 Nonbonded interactions: 80546 Sorted by model distance: nonbonded pdb=" NZ LYS C 121 " pdb=" OXT GLY D 157 " model vdw 1.270 3.120 nonbonded pdb=" NZ LYS C 121 " pdb=" C GLY D 157 " model vdw 1.332 3.350 nonbonded pdb=" O GLY A 39 " pdb=" OG1 THR A 125 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 695 " pdb=" OG SER A 706 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU A 592 " pdb=" NH1 ARG B 155 " model vdw 2.233 3.120 ... (remaining 80541 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 'B' and resid 82 through 157) selection = chain 'D' } 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.090 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.005 0.209 10461 Z= 0.282 Angle : 0.565 13.528 14242 Z= 0.280 Chirality : 0.038 0.142 1591 Planarity : 0.004 0.034 1867 Dihedral : 11.768 69.205 3873 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.00 % Allowed : 7.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1291 helix: 1.74 (0.24), residues: 476 sheet: -1.21 (0.38), residues: 185 loop : -0.12 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.011 0.001 TYR A 603 PHE 0.007 0.001 PHE A 146 TRP 0.006 0.001 TRP C 95 HIS 0.003 0.001 HIS A 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.27 (10460) covalent geometry : angle 0.56532 / 0.28 (14242) hydrogen bonds : bond 0.17714 / 12.16 ( 436) hydrogen bonds : angle 6.52220 / 4.41 ( 1281) Misc. bond : bond 0.08419 / 4.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.226 Fit side-chains REVERT: A 244 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.4391 (m-80) REVERT: A 272 LEU cc_start: 0.8684 (mt) cc_final: 0.8304 (mm) REVERT: A 282 GLN cc_start: 0.8504 (tt0) cc_final: 0.8097 (tp40) REVERT: A 325 ASP cc_start: 0.8016 (t0) cc_final: 0.7807 (t0) REVERT: A 643 MET cc_start: 0.0794 (mmm) cc_final: 0.0458 (mmm) REVERT: A 710 GLN cc_start: 0.2452 (OUTLIER) cc_final: 0.1485 (pp30) REVERT: A 715 LEU cc_start: 0.6883 (tt) cc_final: 0.6603 (tt) REVERT: A 738 MET cc_start: 0.6749 (mtp) cc_final: 0.6539 (mtp) REVERT: A 791 ASN cc_start: 0.7878 (m-40) cc_final: 0.7541 (m-40) REVERT: B 114 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 140 TYR cc_start: 0.8531 (m-10) cc_final: 0.8260 (m-10) REVERT: C 21 TYR cc_start: 0.8274 (p90) cc_final: 0.7656 (p90) REVERT: C 47 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6331 (p90) REVERT: C 67 MET cc_start: 0.7942 (mtt) cc_final: 0.7707 (mtp) REVERT: C 76 HIS cc_start: 0.8354 (t70) cc_final: 0.7837 (t-90) REVERT: C 81 GLU cc_start: 0.8014 (tt0) cc_final: 0.7205 (pt0) REVERT: C 114 ARG cc_start: 0.7093 (tmm160) cc_final: 0.6758 (tmt170) outliers start: 33 outliers final: 15 residues processed: 171 average time/residue: 0.0808 time to fit residues: 19.7699 Evaluate side-chains 132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 117 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 41 GLN A 385 GLN A 522 HIS A 631 ASN A 981 GLN B 102 GLN B 110 GLN C 43 GLN C 103 GLN D 151 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.179021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118706 restraints weight = 13794.401| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.50 r_work: 0.3254 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10461 Z= 0.188 Angle : 0.605 7.015 14242 Z= 0.296 Chirality : 0.041 0.152 1591 Planarity : 0.004 0.040 1867 Dihedral : 6.643 57.860 1441 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.36 % Allowed : 10.08 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1291 helix: 1.52 (0.23), residues: 497 sheet: -1.10 (0.38), residues: 185 loop : -0.25 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 23 TYR 0.013 0.002 TYR A1010 PHE 0.013 0.001 PHE A 146 TRP 0.018 0.001 TRP A 614 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10460) covalent geometry : angle 0.60525 / 0.30 (14242) hydrogen bonds : bond 0.04505 / 3.09 ( 436) hydrogen bonds : angle 5.12861 / 3.52 ( 1281) Misc. bond : bond 0.00529 / 0.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.312 Fit side-chains REVERT: A 244 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5556 (t80) REVERT: A 282 GLN cc_start: 0.8611 (tt0) cc_final: 0.8344 (tp40) REVERT: A 540 ASP cc_start: 0.8647 (p0) cc_final: 0.8395 (p0) REVERT: A 710 GLN cc_start: 0.2315 (OUTLIER) cc_final: 0.1244 (pp30) REVERT: A 715 LEU cc_start: 0.7053 (tt) cc_final: 0.6749 (tt) REVERT: A 791 ASN cc_start: 0.7823 (m-40) cc_final: 0.7476 (m-40) REVERT: A 969 LEU cc_start: 0.8135 (mt) cc_final: 0.7836 (mp) REVERT: A 970 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.7017 (ttm-80) REVERT: A 973 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8329 (pp20) REVERT: B 114 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7856 (mp) REVERT: C 47 HIS cc_start: 0.7158 (OUTLIER) cc_final: 0.6495 (p90) REVERT: C 76 HIS cc_start: 0.8282 (t70) cc_final: 0.7800 (t-90) REVERT: C 80 ASP cc_start: 0.8135 (m-30) cc_final: 0.7930 (m-30) REVERT: C 114 ARG cc_start: 0.7425 (tmm160) cc_final: 0.6175 (tmm160) outliers start: 37 outliers final: 18 residues processed: 148 average time/residue: 0.0735 time to fit residues: 15.8475 Evaluate side-chains 133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 107 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 981 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120180 restraints weight = 13995.207| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.50 r_work: 0.3275 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10461 Z= 0.130 Angle : 0.568 7.226 14242 Z= 0.273 Chirality : 0.039 0.147 1591 Planarity : 0.004 0.043 1867 Dihedral : 6.571 58.658 1436 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.36 % Allowed : 11.44 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1291 helix: 1.66 (0.23), residues: 494 sheet: -1.02 (0.38), residues: 185 loop : -0.27 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 23 TYR 0.018 0.002 TYR C 21 PHE 0.010 0.001 PHE A 146 TRP 0.017 0.001 TRP A 614 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10460) covalent geometry : angle 0.56800 / 0.27 (14242) hydrogen bonds : bond 0.03893 / 2.67 ( 436) hydrogen bonds : angle 4.77282 / 3.26 ( 1281) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5577 (t80) REVERT: A 282 GLN cc_start: 0.8571 (tt0) cc_final: 0.8301 (tp40) REVERT: A 540 ASP cc_start: 0.8644 (p0) cc_final: 0.8341 (p0) REVERT: A 710 GLN cc_start: 0.2260 (OUTLIER) cc_final: 0.1175 (pp30) REVERT: A 715 LEU cc_start: 0.7024 (tt) cc_final: 0.6687 (tt) REVERT: A 765 MET cc_start: 0.0208 (tpt) cc_final: -0.0074 (tpt) REVERT: A 791 ASN cc_start: 0.7865 (m-40) cc_final: 0.7544 (m-40) REVERT: A 969 LEU cc_start: 0.8115 (mt) cc_final: 0.7801 (mp) REVERT: A 970 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.6718 (ttp-110) REVERT: A 973 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8231 (pp20) REVERT: B 114 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 151 ASN cc_start: 0.9345 (m110) cc_final: 0.9047 (m110) REVERT: C 21 TYR cc_start: 0.8056 (p90) cc_final: 0.7584 (p90) REVERT: C 47 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6475 (p90) REVERT: C 76 HIS cc_start: 0.8214 (t70) cc_final: 0.8007 (t-90) REVERT: C 80 ASP cc_start: 0.8090 (m-30) cc_final: 0.7827 (m-30) REVERT: C 114 ARG cc_start: 0.7488 (tmm160) cc_final: 0.7152 (tmm160) outliers start: 37 outliers final: 20 residues processed: 149 average time/residue: 0.0787 time to fit residues: 17.3582 Evaluate side-chains 132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.0770 chunk 34 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.180175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116859 restraints weight = 13899.512| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.10 r_work: 0.3284 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10461 Z= 0.123 Angle : 0.565 8.408 14242 Z= 0.269 Chirality : 0.040 0.279 1591 Planarity : 0.004 0.031 1867 Dihedral : 6.557 59.292 1436 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.09 % Allowed : 12.62 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1291 helix: 1.69 (0.23), residues: 493 sheet: -1.04 (0.37), residues: 185 loop : -0.25 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 23 TYR 0.011 0.001 TYR B 140 PHE 0.010 0.001 PHE A 146 TRP 0.019 0.001 TRP A 614 HIS 0.002 0.000 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10460) covalent geometry : angle 0.56453 / 0.27 (14242) hydrogen bonds : bond 0.03596 / 2.46 ( 436) hydrogen bonds : angle 4.63164 / 3.16 ( 1281) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5630 (t80) REVERT: A 282 GLN cc_start: 0.8556 (tt0) cc_final: 0.8301 (tp40) REVERT: A 540 ASP cc_start: 0.8646 (p0) cc_final: 0.8319 (p0) REVERT: A 710 GLN cc_start: 0.2296 (OUTLIER) cc_final: 0.1094 (pp30) REVERT: A 715 LEU cc_start: 0.7009 (tt) cc_final: 0.6637 (tt) REVERT: A 791 ASN cc_start: 0.7856 (m-40) cc_final: 0.7510 (m-40) REVERT: A 969 LEU cc_start: 0.8092 (mt) cc_final: 0.7771 (mp) REVERT: A 970 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.6738 (ttp-110) REVERT: B 114 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7954 (mp) REVERT: B 139 GLU cc_start: 0.7708 (tp30) cc_final: 0.7458 (tp30) REVERT: B 151 ASN cc_start: 0.9343 (m110) cc_final: 0.9084 (m110) REVERT: C 21 TYR cc_start: 0.8042 (p90) cc_final: 0.7615 (p90) REVERT: C 47 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6340 (p-80) REVERT: C 76 HIS cc_start: 0.8181 (t70) cc_final: 0.7954 (t-90) REVERT: C 80 ASP cc_start: 0.8045 (m-30) cc_final: 0.7812 (m-30) REVERT: C 81 GLU cc_start: 0.8338 (tt0) cc_final: 0.7598 (pt0) REVERT: C 114 ARG cc_start: 0.7522 (tmm160) cc_final: 0.7084 (tmt170) REVERT: C 118 ARG cc_start: 0.9096 (mmp80) cc_final: 0.8847 (mmp80) outliers start: 34 outliers final: 24 residues processed: 140 average time/residue: 0.0826 time to fit residues: 16.7478 Evaluate side-chains 140 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 104 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.182348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.119506 restraints weight = 13839.575| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.20 r_work: 0.3313 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10461 Z= 0.099 Angle : 0.537 6.161 14242 Z= 0.256 Chirality : 0.039 0.207 1591 Planarity : 0.004 0.054 1867 Dihedral : 6.407 57.917 1436 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.36 % Allowed : 12.90 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.24), residues: 1291 helix: 1.79 (0.23), residues: 494 sheet: -1.00 (0.36), residues: 193 loop : -0.19 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 23 TYR 0.011 0.001 TYR A1010 PHE 0.008 0.001 PHE C 63 TRP 0.020 0.001 TRP A 614 HIS 0.002 0.000 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (10460) covalent geometry : angle 0.53736 / 0.26 (14242) hydrogen bonds : bond 0.03230 / 2.20 ( 436) hydrogen bonds : angle 4.44716 / 3.04 ( 1281) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5579 (t80) REVERT: A 282 GLN cc_start: 0.8512 (tt0) cc_final: 0.8246 (tp40) REVERT: A 540 ASP cc_start: 0.8561 (p0) cc_final: 0.8241 (p0) REVERT: A 710 GLN cc_start: 0.2247 (OUTLIER) cc_final: 0.1045 (pp30) REVERT: A 715 LEU cc_start: 0.6942 (tt) cc_final: 0.6580 (tt) REVERT: A 765 MET cc_start: 0.0200 (tpt) cc_final: -0.0073 (tpt) REVERT: A 791 ASN cc_start: 0.7899 (m-40) cc_final: 0.7549 (m-40) REVERT: B 114 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7891 (mp) REVERT: B 139 GLU cc_start: 0.7634 (tp30) cc_final: 0.7395 (tp30) REVERT: C 21 TYR cc_start: 0.8095 (p90) cc_final: 0.7607 (p90) REVERT: C 47 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6278 (p-80) REVERT: C 76 HIS cc_start: 0.8139 (t70) cc_final: 0.7885 (t-90) REVERT: C 80 ASP cc_start: 0.8025 (m-30) cc_final: 0.7784 (m-30) REVERT: C 81 GLU cc_start: 0.8310 (tt0) cc_final: 0.7529 (pt0) REVERT: C 114 ARG cc_start: 0.7544 (tmm160) cc_final: 0.7138 (tmt170) REVERT: D 125 THR cc_start: 0.1369 (m) cc_final: 0.0979 (p) outliers start: 37 outliers final: 23 residues processed: 147 average time/residue: 0.0806 time to fit residues: 17.3633 Evaluate side-chains 138 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 67 optimal weight: 0.0000 chunk 96 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.181770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121645 restraints weight = 13963.234| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.50 r_work: 0.3287 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10461 Z= 0.108 Angle : 0.552 10.433 14242 Z= 0.262 Chirality : 0.039 0.180 1591 Planarity : 0.004 0.036 1867 Dihedral : 6.246 56.072 1433 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.63 % Allowed : 13.26 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1291 helix: 1.81 (0.23), residues: 494 sheet: -0.92 (0.36), residues: 193 loop : -0.18 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 23 TYR 0.011 0.001 TYR B 140 PHE 0.009 0.001 PHE A 146 TRP 0.023 0.001 TRP A 614 HIS 0.006 0.000 HIS A 966 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10460) covalent geometry : angle 0.55214 / 0.26 (14242) hydrogen bonds : bond 0.03193 / 2.18 ( 436) hydrogen bonds : angle 4.39015 / 2.99 ( 1281) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5666 (t80) REVERT: A 282 GLN cc_start: 0.8533 (tt0) cc_final: 0.8272 (tp40) REVERT: A 381 MET cc_start: 0.8200 (tpt) cc_final: 0.7908 (tpt) REVERT: A 710 GLN cc_start: 0.2356 (OUTLIER) cc_final: 0.1090 (pp30) REVERT: A 715 LEU cc_start: 0.6923 (tt) cc_final: 0.6590 (tt) REVERT: A 765 MET cc_start: 0.0263 (tpt) cc_final: 0.0033 (tpt) REVERT: A 791 ASN cc_start: 0.7898 (m-40) cc_final: 0.7545 (m-40) REVERT: B 114 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 139 GLU cc_start: 0.7647 (tp30) cc_final: 0.7427 (tp30) REVERT: C 47 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6285 (p-80) REVERT: C 76 HIS cc_start: 0.8141 (t70) cc_final: 0.7894 (t-90) REVERT: C 80 ASP cc_start: 0.8030 (m-30) cc_final: 0.7755 (m-30) REVERT: C 81 GLU cc_start: 0.8308 (tt0) cc_final: 0.7564 (pt0) REVERT: C 114 ARG cc_start: 0.7602 (tmm160) cc_final: 0.6776 (tmt170) REVERT: C 118 ARG cc_start: 0.9026 (mmp80) cc_final: 0.8538 (mmp80) REVERT: D 125 THR cc_start: 0.1352 (m) cc_final: 0.0969 (p) outliers start: 40 outliers final: 25 residues processed: 145 average time/residue: 0.0802 time to fit residues: 17.0671 Evaluate side-chains 137 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.181289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120592 restraints weight = 13828.717| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.51 r_work: 0.3278 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10461 Z= 0.119 Angle : 0.557 8.986 14242 Z= 0.263 Chirality : 0.039 0.217 1591 Planarity : 0.004 0.041 1867 Dihedral : 6.122 56.687 1431 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.09 % Allowed : 14.62 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.24), residues: 1291 helix: 1.82 (0.23), residues: 494 sheet: -0.91 (0.36), residues: 193 loop : -0.20 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 23 TYR 0.020 0.001 TYR C 21 PHE 0.010 0.001 PHE A 146 TRP 0.025 0.001 TRP A 614 HIS 0.002 0.000 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10460) covalent geometry : angle 0.55744 / 0.26 (14242) hydrogen bonds : bond 0.03210 / 2.21 ( 436) hydrogen bonds : angle 4.36337 / 2.98 ( 1281) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5689 (t80) REVERT: A 282 GLN cc_start: 0.8533 (tt0) cc_final: 0.8274 (tp40) REVERT: A 381 MET cc_start: 0.8208 (tpt) cc_final: 0.7953 (tpt) REVERT: A 710 GLN cc_start: 0.2394 (OUTLIER) cc_final: 0.1074 (pp30) REVERT: A 715 LEU cc_start: 0.6920 (tt) cc_final: 0.6547 (tt) REVERT: A 765 MET cc_start: 0.0398 (tpt) cc_final: 0.0180 (tpt) REVERT: A 791 ASN cc_start: 0.7904 (m-40) cc_final: 0.7554 (m-40) REVERT: B 114 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7946 (mp) REVERT: C 76 HIS cc_start: 0.8166 (t70) cc_final: 0.7906 (t-90) REVERT: C 80 ASP cc_start: 0.8052 (m-30) cc_final: 0.7774 (m-30) REVERT: C 81 GLU cc_start: 0.8314 (tt0) cc_final: 0.7566 (pt0) REVERT: C 114 ARG cc_start: 0.7606 (tmm160) cc_final: 0.6796 (tmt170) REVERT: D 125 THR cc_start: 0.1333 (m) cc_final: 0.0951 (p) outliers start: 34 outliers final: 25 residues processed: 145 average time/residue: 0.0748 time to fit residues: 16.0719 Evaluate side-chains 139 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119649 restraints weight = 13894.321| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.45 r_work: 0.3267 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10461 Z= 0.134 Angle : 0.572 6.690 14242 Z= 0.270 Chirality : 0.039 0.178 1591 Planarity : 0.004 0.047 1867 Dihedral : 6.173 57.907 1431 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.91 % Allowed : 15.08 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1291 helix: 1.79 (0.23), residues: 493 sheet: -1.00 (0.37), residues: 185 loop : -0.24 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 23 TYR 0.016 0.001 TYR C 21 PHE 0.020 0.001 PHE D 126 TRP 0.018 0.001 TRP A 614 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (10460) covalent geometry : angle 0.57231 / 0.27 (14242) hydrogen bonds : bond 0.03310 / 2.28 ( 436) hydrogen bonds : angle 4.36980 / 2.99 ( 1281) Misc. bond : bond 0.00069 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5685 (t80) REVERT: A 282 GLN cc_start: 0.8567 (tt0) cc_final: 0.8305 (tp40) REVERT: A 381 MET cc_start: 0.8238 (tpt) cc_final: 0.7945 (tpt) REVERT: A 710 GLN cc_start: 0.2532 (OUTLIER) cc_final: 0.1151 (pp30) REVERT: A 715 LEU cc_start: 0.6897 (tt) cc_final: 0.6559 (tt) REVERT: A 765 MET cc_start: 0.0429 (tpt) cc_final: 0.0222 (tpt) REVERT: A 791 ASN cc_start: 0.7879 (m-40) cc_final: 0.7544 (m-40) REVERT: B 114 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7930 (mp) REVERT: C 76 HIS cc_start: 0.8189 (t70) cc_final: 0.7925 (t-90) REVERT: C 80 ASP cc_start: 0.8076 (m-30) cc_final: 0.7785 (m-30) REVERT: C 81 GLU cc_start: 0.8357 (tt0) cc_final: 0.7604 (pt0) REVERT: C 114 ARG cc_start: 0.7619 (tmm160) cc_final: 0.6812 (tmt170) REVERT: C 118 ARG cc_start: 0.9040 (mmp80) cc_final: 0.8422 (mmp80) REVERT: D 125 THR cc_start: 0.1288 (m) cc_final: 0.0935 (p) outliers start: 32 outliers final: 26 residues processed: 139 average time/residue: 0.0912 time to fit residues: 18.0752 Evaluate side-chains 141 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.181161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121474 restraints weight = 13922.901| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.30 r_work: 0.3288 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10461 Z= 0.121 Angle : 0.566 7.776 14242 Z= 0.267 Chirality : 0.039 0.182 1591 Planarity : 0.004 0.042 1867 Dihedral : 6.148 57.925 1431 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.18 % Allowed : 15.17 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1291 helix: 1.89 (0.24), residues: 487 sheet: -1.01 (0.37), residues: 185 loop : -0.19 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 23 TYR 0.022 0.001 TYR C 21 PHE 0.017 0.001 PHE D 126 TRP 0.029 0.001 TRP A 614 HIS 0.003 0.000 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10460) covalent geometry : angle 0.56594 / 0.27 (14242) hydrogen bonds : bond 0.03194 / 2.20 ( 436) hydrogen bonds : angle 4.30390 / 2.95 ( 1281) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5704 (t80) REVERT: A 282 GLN cc_start: 0.8531 (tt0) cc_final: 0.8280 (tp40) REVERT: A 381 MET cc_start: 0.8226 (tpt) cc_final: 0.7987 (tpt) REVERT: A 580 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: A 710 GLN cc_start: 0.2223 (OUTLIER) cc_final: 0.0848 (pp30) REVERT: A 715 LEU cc_start: 0.6891 (tt) cc_final: 0.6559 (tt) REVERT: A 791 ASN cc_start: 0.7857 (m-40) cc_final: 0.7234 (t0) REVERT: B 114 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7816 (mp) REVERT: C 21 TYR cc_start: 0.7785 (p90) cc_final: 0.7408 (p90) REVERT: C 76 HIS cc_start: 0.8164 (t70) cc_final: 0.7899 (t-90) REVERT: C 80 ASP cc_start: 0.8091 (m-30) cc_final: 0.7751 (m-30) REVERT: C 81 GLU cc_start: 0.8338 (tt0) cc_final: 0.7597 (pt0) REVERT: C 114 ARG cc_start: 0.7630 (tmm160) cc_final: 0.6840 (tmt170) REVERT: C 118 ARG cc_start: 0.9020 (mmp80) cc_final: 0.8423 (mmp80) outliers start: 35 outliers final: 29 residues processed: 139 average time/residue: 0.0880 time to fit residues: 17.8608 Evaluate side-chains 145 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 0.0170 chunk 2 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.181736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121631 restraints weight = 13754.557| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.48 r_work: 0.3288 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10461 Z= 0.109 Angle : 0.564 7.733 14242 Z= 0.265 Chirality : 0.039 0.180 1591 Planarity : 0.004 0.043 1867 Dihedral : 6.058 57.105 1431 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.63 % Allowed : 15.99 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1291 helix: 1.91 (0.23), residues: 488 sheet: -0.99 (0.37), residues: 185 loop : -0.17 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 23 TYR 0.017 0.001 TYR C 21 PHE 0.018 0.001 PHE D 126 TRP 0.025 0.001 TRP A 614 HIS 0.004 0.000 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10460) covalent geometry : angle 0.56422 / 0.27 (14242) hydrogen bonds : bond 0.03032 / 2.07 ( 436) hydrogen bonds : angle 4.24856 / 2.91 ( 1281) Misc. bond : bond 0.00054 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 282 GLN cc_start: 0.8529 (tt0) cc_final: 0.8279 (tp40) REVERT: A 381 MET cc_start: 0.8205 (tpt) cc_final: 0.7937 (tpt) REVERT: A 710 GLN cc_start: 0.2206 (OUTLIER) cc_final: 0.0846 (pp30) REVERT: A 715 LEU cc_start: 0.6869 (tt) cc_final: 0.6561 (tt) REVERT: A 791 ASN cc_start: 0.7799 (m-40) cc_final: 0.7371 (t0) REVERT: B 88 ASN cc_start: 0.8174 (t0) cc_final: 0.7097 (t0) REVERT: C 21 TYR cc_start: 0.7723 (p90) cc_final: 0.7454 (p90) REVERT: C 75 TYR cc_start: 0.7407 (t80) cc_final: 0.7093 (t80) REVERT: C 76 HIS cc_start: 0.8113 (t70) cc_final: 0.7842 (t-90) REVERT: C 80 ASP cc_start: 0.8103 (m-30) cc_final: 0.7759 (m-30) REVERT: C 81 GLU cc_start: 0.8354 (tt0) cc_final: 0.7602 (pt0) REVERT: C 114 ARG cc_start: 0.7650 (tmm160) cc_final: 0.6815 (tmt170) REVERT: C 118 ARG cc_start: 0.9016 (mmp80) cc_final: 0.8135 (mmp80) REVERT: C 119 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7882 (mt-10) outliers start: 29 outliers final: 26 residues processed: 140 average time/residue: 0.0786 time to fit residues: 16.1276 Evaluate side-chains 143 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 0.1980 chunk 108 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 0.0040 overall best weight: 0.6512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.181618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122059 restraints weight = 13851.422| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.28 r_work: 0.3299 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10461 Z= 0.118 Angle : 0.568 7.947 14242 Z= 0.269 Chirality : 0.039 0.179 1591 Planarity : 0.004 0.041 1867 Dihedral : 5.828 57.188 1427 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.72 % Allowed : 16.08 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1291 helix: 1.92 (0.23), residues: 487 sheet: -1.02 (0.37), residues: 185 loop : -0.19 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 23 TYR 0.016 0.001 TYR C 21 PHE 0.017 0.001 PHE D 126 TRP 0.026 0.001 TRP A 614 HIS 0.004 0.000 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10460) covalent geometry : angle 0.56808 / 0.27 (14242) hydrogen bonds : bond 0.03102 / 2.12 ( 436) hydrogen bonds : angle 4.24672 / 2.91 ( 1281) Misc. bond : bond 0.00059 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.90 seconds wall clock time: 36 minutes 2.80 seconds (2162.80 seconds total)