Starting phenix.real_space_refine on Fri Sep 11 14:44:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pqu_20453/09_2026/6pqu_20453.cif" } resolution = 3.3 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= 0.004 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 2 6.06 5 P 124 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5962 2.51 5 N 1728 2.21 5 O 2150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 633 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1629 SG CYS A 240 84.803 102.677 59.207 1.00119.06 S ATOM 1655 SG CYS A 243 87.305 102.753 61.798 1.00116.38 S Restraints were copied for chains: E, F, G, H Time building chain proxies: 3.36, per 1000 atoms: 0.34 Number of scatterers: 10004 At special positions: 0 Unit cell: (110.25, 118.65, 114.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 2 19.00 S 34 16.00 P 124 15.00 Mg 2 11.99 O 2150 8.00 N 1728 7.00 C 5962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 288.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 240 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 408 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 413 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 243 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 240 " Number of angles added : 4 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 52.4% alpha, 12.8% beta 61 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.860A pdb=" N GLY A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.698A pdb=" N GLN A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 106 removed outlier: 3.618A pdb=" N PHE A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.948A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 175' Processing helix chain 'A' and resid 186 through 204 removed outlier: 3.633A pdb=" N VAL A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.671A pdb=" N THR A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 4.052A pdb=" N ILE A 286 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.748A pdb=" N LEU A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.650A pdb=" N ALA A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 4.061A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.815A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.965A pdb=" N ILE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 454 through 468 removed outlier: 3.533A pdb=" N ASN A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.859A pdb=" N GLY E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 53 Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.698A pdb=" N GLN E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 106 removed outlier: 3.618A pdb=" N PHE E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.949A pdb=" N TYR E 174 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 186 through 204 removed outlier: 3.632A pdb=" N VAL E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 264 through 272 removed outlier: 3.670A pdb=" N THR E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 290 removed outlier: 4.051A pdb=" N ILE E 286 " --> pdb=" O CYS E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 321 removed outlier: 3.747A pdb=" N LEU E 305 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 346 removed outlier: 3.650A pdb=" N ALA E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 removed outlier: 4.062A pdb=" N THR E 351 " --> pdb=" O PHE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.815A pdb=" N ILE E 362 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.966A pdb=" N ILE E 418 " --> pdb=" O GLY E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 447 Processing helix chain 'E' and resid 454 through 468 removed outlier: 3.519A pdb=" N ASN E 458 " --> pdb=" O ARG E 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 82 removed outlier: 4.250A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 165 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 156 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 removed outlier: 5.040A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 116 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 217 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 124 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE A 223 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 79 through 82 removed outlier: 4.249A pdb=" N GLN E 179 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU E 154 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL E 165 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU E 156 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 127 through 128 removed outlier: 5.039A pdb=" N LEU E 151 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLY E 123 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 121 " --> pdb=" O PRO E 153 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU E 116 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS E 217 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE E 124 " --> pdb=" O THR E 221 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE E 223 " --> pdb=" O PHE E 124 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 152 hydrogen bonds 304 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2297 1.33 - 1.45: 2825 1.45 - 1.58: 5025 1.58 - 1.70: 241 1.70 - 1.82: 52 Bond restraints: 10440 Sorted by residual: bond pdb=" N9 DG C 24 " pdb=" C8 DG C 24 " ideal model delta sigma weight residual 1.374 1.348 0.026 7.00e-03 2.04e+04 1.38e+01 bond pdb=" N9 DG G 24 " pdb=" C8 DG G 24 " ideal model delta sigma weight residual 1.374 1.348 0.026 7.00e-03 2.04e+04 1.37e+01 bond pdb=" C3' DG H 6 " pdb=" O3' DG H 6 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" C3' DG D 6 " pdb=" O3' DG D 6 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C3' DG G 23 " pdb=" O3' DG G 23 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.23e+01 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 14333 2.68 - 5.37: 253 5.37 - 8.05: 34 8.05 - 10.73: 2 10.73 - 13.41: 2 Bond angle restraints: 14624 Sorted by residual: angle pdb=" N SER A 453 " pdb=" CA SER A 453 " pdb=" C SER A 453 " ideal model delta sigma weight residual 110.80 124.21 -13.41 2.13e+00 2.20e-01 3.97e+01 angle pdb=" N SER E 453 " pdb=" CA SER E 453 " pdb=" C SER E 453 " ideal model delta sigma weight residual 110.80 124.19 -13.39 2.13e+00 2.20e-01 3.95e+01 angle pdb=" C SER E 453 " pdb=" N ARG E 454 " pdb=" CA ARG E 454 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C SER A 453 " pdb=" N ARG A 454 " pdb=" CA ARG A 454 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" N GLN A 455 " pdb=" CA GLN A 455 " pdb=" C GLN A 455 " ideal model delta sigma weight residual 111.36 105.71 5.65 1.09e+00 8.42e-01 2.68e+01 ... (remaining 14619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 5100 27.97 - 55.94: 784 55.94 - 83.91: 114 83.91 - 111.88: 0 111.88 - 139.85: 2 Dihedral angle restraints: 6000 sinusoidal: 3248 harmonic: 2752 Sorted by residual: dihedral pdb=" CA GLN A 499 " pdb=" C GLN A 499 " pdb=" N ASP A 500 " pdb=" CA ASP A 500 " ideal model delta harmonic sigma weight residual -180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLN E 499 " pdb=" C GLN E 499 " pdb=" N ASP E 500 " pdb=" CA ASP E 500 " ideal model delta harmonic sigma weight residual -180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" N ARG A 454 " pdb=" C ARG A 454 " pdb=" CA ARG A 454 " pdb=" CB ARG A 454 " ideal model delta harmonic sigma weight residual 122.80 134.17 -11.37 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 5997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1402 0.077 - 0.154: 248 0.154 - 0.231: 12 0.231 - 0.308: 0 0.308 - 0.385: 4 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA SER A 453 " pdb=" N SER A 453 " pdb=" C SER A 453 " pdb=" CB SER A 453 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA SER E 453 " pdb=" N SER E 453 " pdb=" C SER E 453 " pdb=" CB SER E 453 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA ARG A 454 " pdb=" N ARG A 454 " pdb=" C ARG A 454 " pdb=" CB ARG A 454 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 1663 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG G 20 " -0.030 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 DG G 20 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG G 20 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG G 20 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG G 20 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG G 20 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG G 20 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG G 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG G 20 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG G 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG G 20 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG G 20 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 20 " -0.030 2.00e-02 2.50e+03 1.22e-02 4.44e+00 pdb=" N9 DG C 20 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG C 20 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG C 20 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG C 20 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG C 20 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG C 20 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG C 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 20 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG C 20 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG C 20 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG C 20 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 380 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO E 381 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 381 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 381 " 0.026 5.00e-02 4.00e+02 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.60: 195 2.60 - 3.24: 10151 3.24 - 3.87: 20321 3.87 - 4.51: 26369 4.51 - 5.14: 39722 Nonbonded interactions: 96758 Sorted by model distance: nonbonded pdb=" OD1 ASP E 125 " pdb="MG MG E 601 " model vdw 1.970 2.170 nonbonded pdb=" OD2 ASP A 224 " pdb="MG MG A 601 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP A 125 " pdb="MG MG A 601 " model vdw 2.015 2.170 nonbonded pdb=" OD2 ASP E 224 " pdb="MG MG E 601 " model vdw 2.027 2.170 nonbonded pdb=" OP2 DC D 5 " pdb=" OG SER E 61 " model vdw 2.202 3.040 ... (remaining 96753 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 10448 Z= 0.596 Angle : 0.987 17.484 14628 Z= 0.686 Chirality : 0.057 0.385 1666 Planarity : 0.005 0.046 1416 Dihedral : 23.511 139.846 4208 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.39 % Favored : 97.39 % Rotamer: Outliers : 1.21 % Allowed : 9.90 % Favored : 88.89 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.20), residues: 920 helix: -2.64 (0.17), residues: 464 sheet: -2.83 (0.57), residues: 58 loop : -3.66 (0.22), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 276 TYR 0.014 0.002 TYR E 394 PHE 0.022 0.003 PHE A 383 TRP 0.011 0.002 TRP E 122 HIS 0.004 0.001 HIS E 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00889 / 0.59 (10440) covalent geometry : angle 0.96058 / 0.68 (14624) hydrogen bonds : bond 0.15096 / 9.80 ( 522) hydrogen bonds : angle 6.92307 / 4.80 ( 1384) metal coordination : bond 0.06810 / 4.26 ( 8) metal coordination : angle 13.81592 / 6.80 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7061 (m-40) cc_final: 0.6593 (t0) REVERT: A 304 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: E 304 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: E 426 ILE cc_start: 0.7949 (tt) cc_final: 0.7723 (tt) outliers start: 10 outliers final: 4 residues processed: 120 average time/residue: 0.0956 time to fit residues: 16.7303 Evaluate side-chains 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 404 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 129 ASN A 339 ASN E 113 ASN E 129 ASN E 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.235280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.180760 restraints weight = 13893.818| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 2.44 r_work: 0.4422 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10448 Z= 0.174 Angle : 0.766 7.543 14628 Z= 0.426 Chirality : 0.047 0.236 1666 Planarity : 0.005 0.058 1416 Dihedral : 27.006 138.714 2366 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.02 % Favored : 95.76 % Rotamer: Outliers : 2.42 % Allowed : 12.56 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.24), residues: 920 helix: -0.83 (0.22), residues: 462 sheet: -1.76 (0.70), residues: 60 loop : -3.05 (0.24), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 485 TYR 0.029 0.002 TYR E 488 PHE 0.020 0.002 PHE A 345 TRP 0.012 0.001 TRP A 122 HIS 0.006 0.001 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (10440) covalent geometry : angle 0.76100 / 0.43 (14624) hydrogen bonds : bond 0.05677 / 3.87 ( 522) hydrogen bonds : angle 4.89776 / 3.37 ( 1384) metal coordination : bond 0.02777 / 1.85 ( 8) metal coordination : angle 5.37524 / 2.64 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.382 Fit side-chains REVERT: A 199 ASP cc_start: 0.7606 (m-30) cc_final: 0.7346 (m-30) REVERT: A 304 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: E 304 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7488 (tm-30) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 0.0959 time to fit residues: 15.3548 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 404 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.233380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.179122 restraints weight = 13854.108| |-----------------------------------------------------------------------------| r_work (start): 0.4607 rms_B_bonded: 2.32 r_work: 0.4404 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10448 Z= 0.199 Angle : 0.731 7.810 14628 Z= 0.403 Chirality : 0.046 0.167 1666 Planarity : 0.005 0.061 1416 Dihedral : 26.831 136.008 2365 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.98 % Favored : 93.80 % Rotamer: Outliers : 3.26 % Allowed : 16.55 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.25), residues: 920 helix: -0.29 (0.23), residues: 460 sheet: -1.70 (0.67), residues: 60 loop : -2.88 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 100 TYR 0.022 0.002 TYR E 488 PHE 0.019 0.002 PHE E 345 TRP 0.009 0.001 TRP A 122 HIS 0.004 0.001 HIS E 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (10440) covalent geometry : angle 0.72477 / 0.40 (14624) hydrogen bonds : bond 0.05273 / 3.60 ( 522) hydrogen bonds : angle 4.66724 / 3.22 ( 1384) metal coordination : bond 0.02809 / 1.92 ( 8) metal coordination : angle 5.94665 / 2.92 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.319 Fit side-chains REVERT: A 199 ASP cc_start: 0.7702 (m-30) cc_final: 0.7425 (m-30) REVERT: A 304 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: A 424 VAL cc_start: 0.7740 (OUTLIER) cc_final: 0.7404 (t) REVERT: E 199 ASP cc_start: 0.7454 (m-30) cc_final: 0.7201 (m-30) REVERT: E 280 MET cc_start: 0.8667 (tpt) cc_final: 0.8389 (tpt) REVERT: E 304 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: E 424 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7307 (t) outliers start: 27 outliers final: 10 residues processed: 112 average time/residue: 0.0807 time to fit residues: 13.7141 Evaluate side-chains 93 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.236957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.183530 restraints weight = 13943.154| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 2.31 r_work: 0.4462 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10448 Z= 0.153 Angle : 0.692 9.947 14628 Z= 0.380 Chirality : 0.045 0.235 1666 Planarity : 0.004 0.053 1416 Dihedral : 26.701 135.201 2363 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.76 % Favored : 94.02 % Rotamer: Outliers : 3.74 % Allowed : 17.27 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.25), residues: 920 helix: -0.03 (0.23), residues: 460 sheet: -1.45 (0.68), residues: 60 loop : -2.62 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.028 0.002 TYR A 288 PHE 0.013 0.002 PHE E 180 TRP 0.009 0.001 TRP A 122 HIS 0.004 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (10440) covalent geometry : angle 0.68393 / 0.38 (14624) hydrogen bonds : bond 0.04620 / 3.14 ( 522) hydrogen bonds : angle 4.38565 / 3.02 ( 1384) metal coordination : bond 0.02228 / 1.50 ( 8) metal coordination : angle 6.21262 / 3.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.287 Fit side-chains REVERT: A 199 ASP cc_start: 0.7587 (m-30) cc_final: 0.7352 (m-30) REVERT: A 304 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: A 424 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7431 (t) REVERT: E 116 LEU cc_start: 0.8372 (mt) cc_final: 0.8061 (mp) REVERT: E 280 MET cc_start: 0.8654 (tpt) cc_final: 0.8407 (tpt) REVERT: E 304 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: E 424 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7328 (t) outliers start: 31 outliers final: 16 residues processed: 110 average time/residue: 0.0883 time to fit residues: 14.7473 Evaluate side-chains 102 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.238696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.184269 restraints weight = 13869.241| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 2.28 r_work: 0.4464 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10448 Z= 0.145 Angle : 0.662 7.739 14628 Z= 0.367 Chirality : 0.044 0.344 1666 Planarity : 0.004 0.050 1416 Dihedral : 26.588 134.820 2363 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.35 % Allowed : 18.24 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.26), residues: 920 helix: 0.26 (0.23), residues: 458 sheet: -1.14 (0.69), residues: 60 loop : -2.46 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.017 0.002 TYR A 288 PHE 0.012 0.001 PHE A 180 TRP 0.008 0.001 TRP E 122 HIS 0.006 0.001 HIS E 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (10440) covalent geometry : angle 0.65524 / 0.37 (14624) hydrogen bonds : bond 0.04322 / 2.94 ( 522) hydrogen bonds : angle 4.19058 / 2.89 ( 1384) metal coordination : bond 0.01932 / 1.33 ( 8) metal coordination : angle 5.80082 / 2.86 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.335 Fit side-chains REVERT: A 99 ASN cc_start: 0.7219 (m-40) cc_final: 0.6603 (t0) REVERT: A 304 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: A 424 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7399 (t) REVERT: A 446 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 488 TYR cc_start: 0.5689 (m-10) cc_final: 0.5080 (m-10) REVERT: E 116 LEU cc_start: 0.8410 (mt) cc_final: 0.8052 (mp) REVERT: E 193 GLU cc_start: 0.6966 (tp30) cc_final: 0.5978 (tp30) REVERT: E 304 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: E 424 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7342 (t) outliers start: 36 outliers final: 21 residues processed: 124 average time/residue: 0.0826 time to fit residues: 15.6204 Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.0010 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.237144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.183979 restraints weight = 13959.061| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 2.33 r_work: 0.4443 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10448 Z= 0.166 Angle : 0.663 8.254 14628 Z= 0.365 Chirality : 0.044 0.175 1666 Planarity : 0.004 0.049 1416 Dihedral : 26.573 134.807 2363 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.14 % Allowed : 19.69 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.26), residues: 920 helix: 0.28 (0.23), residues: 458 sheet: -1.17 (0.69), residues: 60 loop : -2.44 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.033 0.002 TYR A 288 PHE 0.013 0.001 PHE E 180 TRP 0.005 0.001 TRP E 122 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (10440) covalent geometry : angle 0.65747 / 0.36 (14624) hydrogen bonds : bond 0.04366 / 2.97 ( 522) hydrogen bonds : angle 4.19281 / 2.89 ( 1384) metal coordination : bond 0.01820 / 1.26 ( 8) metal coordination : angle 5.24572 / 2.59 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.272 Fit side-chains REVERT: A 99 ASN cc_start: 0.7203 (m-40) cc_final: 0.6582 (t0) REVERT: A 304 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: A 424 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7445 (t) REVERT: A 446 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7411 (tm-30) REVERT: E 116 LEU cc_start: 0.8373 (mt) cc_final: 0.8026 (mp) REVERT: E 193 GLU cc_start: 0.7018 (tp30) cc_final: 0.5944 (tp30) REVERT: E 280 MET cc_start: 0.8667 (tpt) cc_final: 0.8436 (tpp) REVERT: E 304 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: E 361 LEU cc_start: 0.6082 (tp) cc_final: 0.5826 (tt) REVERT: E 424 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7370 (t) outliers start: 26 outliers final: 17 residues processed: 116 average time/residue: 0.0837 time to fit residues: 14.4928 Evaluate side-chains 113 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 40.0000 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.238170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.185105 restraints weight = 13973.499| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 2.42 r_work: 0.4457 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10448 Z= 0.154 Angle : 0.658 9.337 14628 Z= 0.362 Chirality : 0.043 0.293 1666 Planarity : 0.004 0.048 1416 Dihedral : 26.511 134.680 2363 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.26 % Allowed : 20.17 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.26), residues: 920 helix: 0.41 (0.23), residues: 458 sheet: -1.03 (0.71), residues: 60 loop : -2.37 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.027 0.002 TYR A 288 PHE 0.015 0.001 PHE A 344 TRP 0.005 0.001 TRP E 122 HIS 0.004 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (10440) covalent geometry : angle 0.65229 / 0.36 (14624) hydrogen bonds : bond 0.04170 / 2.83 ( 522) hydrogen bonds : angle 4.15153 / 2.88 ( 1384) metal coordination : bond 0.01571 / 1.10 ( 8) metal coordination : angle 5.10658 / 2.51 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.195 Fit side-chains REVERT: A 99 ASN cc_start: 0.7174 (m-40) cc_final: 0.6565 (t0) REVERT: A 304 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: A 424 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7453 (t) REVERT: A 446 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7405 (tm-30) REVERT: E 116 LEU cc_start: 0.8342 (mt) cc_final: 0.7984 (mp) REVERT: E 193 GLU cc_start: 0.7007 (tp30) cc_final: 0.5933 (tp30) REVERT: E 219 MET cc_start: 0.7935 (mpp) cc_final: 0.7708 (mpp) REVERT: E 304 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: E 361 LEU cc_start: 0.6217 (tp) cc_final: 0.5968 (tt) REVERT: E 424 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7450 (t) REVERT: E 446 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7385 (tm-30) outliers start: 27 outliers final: 18 residues processed: 114 average time/residue: 0.0816 time to fit residues: 13.8053 Evaluate side-chains 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 424 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.233048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.177712 restraints weight = 13866.681| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 2.33 r_work: 0.4387 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 10448 Z= 0.259 Angle : 0.748 9.476 14628 Z= 0.403 Chirality : 0.047 0.192 1666 Planarity : 0.004 0.047 1416 Dihedral : 26.534 134.146 2363 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.14 % Allowed : 21.38 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.26), residues: 920 helix: 0.10 (0.23), residues: 458 sheet: -1.12 (0.74), residues: 60 loop : -2.51 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 100 TYR 0.025 0.002 TYR A 288 PHE 0.015 0.002 PHE A 180 TRP 0.006 0.001 TRP E 400 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.26 (10440) covalent geometry : angle 0.74481 / 0.40 (14624) hydrogen bonds : bond 0.05093 / 3.47 ( 522) hydrogen bonds : angle 4.45638 / 3.10 ( 1384) metal coordination : bond 0.02304 / 1.64 ( 8) metal coordination : angle 4.25736 / 2.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.347 Fit side-chains REVERT: A 99 ASN cc_start: 0.7233 (m-40) cc_final: 0.6591 (t0) REVERT: A 304 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: A 424 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7482 (t) REVERT: A 446 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7485 (tm-30) REVERT: E 99 ASN cc_start: 0.7106 (m-40) cc_final: 0.6599 (t0) REVERT: E 116 LEU cc_start: 0.8414 (mt) cc_final: 0.8044 (mp) REVERT: E 304 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: E 446 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7515 (tm-30) outliers start: 26 outliers final: 17 residues processed: 113 average time/residue: 0.0929 time to fit residues: 15.5899 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 468 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.237712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.182374 restraints weight = 13855.416| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 2.40 r_work: 0.4461 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10448 Z= 0.146 Angle : 0.665 8.431 14628 Z= 0.364 Chirality : 0.043 0.232 1666 Planarity : 0.004 0.048 1416 Dihedral : 26.411 133.043 2363 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.78 % Allowed : 21.98 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 920 helix: 0.55 (0.24), residues: 446 sheet: -0.89 (0.73), residues: 60 loop : -2.30 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.021 0.001 TYR A 288 PHE 0.016 0.001 PHE A 344 TRP 0.007 0.001 TRP E 122 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (10440) covalent geometry : angle 0.66079 / 0.36 (14624) hydrogen bonds : bond 0.04058 / 2.75 ( 522) hydrogen bonds : angle 4.16401 / 2.88 ( 1384) metal coordination : bond 0.01344 / 0.97 ( 8) metal coordination : angle 4.77854 / 2.36 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.200 Fit side-chains REVERT: A 99 ASN cc_start: 0.7099 (m-40) cc_final: 0.6494 (t0) REVERT: A 197 MET cc_start: 0.7859 (mtp) cc_final: 0.7434 (tpp) REVERT: A 304 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: A 424 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 446 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7507 (tm-30) REVERT: E 193 GLU cc_start: 0.6991 (tp30) cc_final: 0.5984 (tp30) REVERT: E 304 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: E 446 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7507 (tm-30) outliers start: 23 outliers final: 17 residues processed: 110 average time/residue: 0.0840 time to fit residues: 13.9410 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 468 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.239057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.185120 restraints weight = 13791.980| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 2.44 r_work: 0.4329 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10448 Z= 0.140 Angle : 0.651 8.560 14628 Z= 0.355 Chirality : 0.042 0.195 1666 Planarity : 0.004 0.048 1416 Dihedral : 26.313 133.361 2363 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.42 % Allowed : 22.83 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.26), residues: 920 helix: 0.65 (0.23), residues: 448 sheet: -0.72 (0.76), residues: 60 loop : -2.20 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 342 TYR 0.020 0.001 TYR A 288 PHE 0.014 0.001 PHE A 344 TRP 0.009 0.001 TRP E 122 HIS 0.007 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (10440) covalent geometry : angle 0.64606 / 0.35 (14624) hydrogen bonds : bond 0.03989 / 2.71 ( 522) hydrogen bonds : angle 4.07128 / 2.81 ( 1384) metal coordination : bond 0.02044 / 1.61 ( 8) metal coordination : angle 4.89837 / 2.37 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.325 Fit side-chains REVERT: A 99 ASN cc_start: 0.7138 (m-40) cc_final: 0.6531 (t0) REVERT: A 193 GLU cc_start: 0.6734 (tp30) cc_final: 0.6526 (tp30) REVERT: A 197 MET cc_start: 0.7817 (mtp) cc_final: 0.7607 (tpp) REVERT: A 304 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: A 424 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.7427 (t) REVERT: A 446 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7484 (tm-30) REVERT: E 304 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: E 446 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7415 (tm-30) outliers start: 20 outliers final: 14 residues processed: 108 average time/residue: 0.0861 time to fit residues: 14.0077 Evaluate side-chains 107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 7.9990 chunk 89 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.240084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.185442 restraints weight = 13952.619| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 2.47 r_work: 0.4346 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10448 Z= 0.135 Angle : 0.638 8.170 14628 Z= 0.347 Chirality : 0.042 0.183 1666 Planarity : 0.004 0.049 1416 Dihedral : 26.241 133.622 2362 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.78 % Allowed : 22.34 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.26), residues: 920 helix: 0.76 (0.24), residues: 446 sheet: -0.68 (0.73), residues: 60 loop : -2.19 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.018 0.001 TYR A 288 PHE 0.015 0.001 PHE A 344 TRP 0.007 0.001 TRP E 122 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (10440) covalent geometry : angle 0.63373 / 0.35 (14624) hydrogen bonds : bond 0.03838 / 2.59 ( 522) hydrogen bonds : angle 4.00624 / 2.78 ( 1384) metal coordination : bond 0.01282 / 0.96 ( 8) metal coordination : angle 4.44821 / 2.24 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.45 seconds wall clock time: 43 minutes 29.42 seconds (2609.42 seconds total)