Starting phenix.real_space_refine on Wed Mar 4 01:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqu_20453/03_2026/6pqu_20453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqu_20453/03_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_20453/03_2026/6pqu_20453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqu_20453/03_2026/6pqu_20453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqu_20453/03_2026/6pqu_20453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqu_20453/03_2026/6pqu_20453.map" } 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-dev-5986/lib/python3.9/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: 2.68, per 1000 atoms: 0.27 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: 0.99 Conformation dependent library (CDL) restraints added in 386.1 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: 1.39 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: 1.90 Time building geometry restraints manager: 1.24 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=" C CYS A 175 " pdb=" N ARG A 176 " ideal model delta sigma weight residual 1.331 1.377 -0.046 1.63e-02 3.76e+03 7.92e+00 bond pdb=" C CYS E 175 " pdb=" N ARG E 176 " ideal model delta sigma weight residual 1.331 1.376 -0.045 1.63e-02 3.76e+03 7.48e+00 bond pdb=" N SER E 453 " pdb=" CA SER E 453 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.11e+00 bond pdb=" N SER A 453 " pdb=" CA SER A 453 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.81e+00 bond pdb=" N ARG E 454 " pdb=" CA ARG E 454 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.40e+00 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 14375 2.68 - 5.37: 211 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=" O3' DA H 11 " pdb=" C3' DA H 11 " pdb=" C2' DA H 11 " ideal model delta sigma weight residual 111.50 103.56 7.94 1.50e+00 4.44e-01 2.80e+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: 1469 0.077 - 0.154: 183 0.154 - 0.231: 10 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: 0.01 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: 1.060 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.060 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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= 0.376 Angle : 0.926 17.484 14628 Z= 0.516 Chirality : 0.053 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 covalent geometry : bond 0.00840 (10440) covalent geometry : angle 0.89755 (14624) hydrogen bonds : bond 0.15096 ( 522) hydrogen bonds : angle 6.92307 ( 1384) metal coordination : bond 0.06810 ( 8) metal coordination : angle 13.81592 ( 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 : 0.332 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: 0.0978 time to fit residues: 16.8366 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 : 0.304 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 10.0000 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5069 r_free = 0.5069 target = 0.237053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.184033 restraints weight = 13903.177| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 2.36 r_work: 0.4465 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10448 Z= 0.164 Angle : 0.701 7.523 14628 Z= 0.380 Chirality : 0.041 0.168 1666 Planarity : 0.005 0.058 1416 Dihedral : 26.628 134.066 2366 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.02 % Favored : 95.76 % Rotamer: Outliers : 3.02 % Allowed : 11.84 % Favored : 85.14 % 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: -2.46 (0.24), residues: 920 helix: -0.52 (0.22), residues: 462 sheet: -1.93 (0.67), residues: 60 loop : -2.97 (0.24), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 454 TYR 0.026 0.002 TYR A 266 PHE 0.014 0.002 PHE A 345 TRP 0.014 0.001 TRP A 122 HIS 0.003 0.001 HIS E 307 Details of bonding type rmsd covalent geometry : bond 0.00360 (10440) covalent geometry : angle 0.69037 (14624) hydrogen bonds : bond 0.04544 ( 522) hydrogen bonds : angle 4.65610 ( 1384) metal coordination : bond 0.00917 ( 8) metal coordination : angle 7.36952 ( 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 128 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.346 Fit side-chains REVERT: A 199 ASP cc_start: 0.7549 (m-30) cc_final: 0.7307 (m-30) REVERT: A 304 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: E 199 ASP cc_start: 0.7444 (m-30) cc_final: 0.7173 (m-30) REVERT: E 236 SER cc_start: 0.1282 (OUTLIER) cc_final: 0.1060 (p) REVERT: E 291 ASP cc_start: 0.6951 (p0) cc_final: 0.6602 (p0) REVERT: E 304 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: E 426 ILE cc_start: 0.8115 (tt) cc_final: 0.7839 (tt) outliers start: 25 outliers final: 10 residues processed: 121 average time/residue: 0.0981 time to fit residues: 17.1770 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 304 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 492 THR 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 492 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN E 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.235602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.181722 restraints weight = 13866.893| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 2.28 r_work: 0.4425 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10448 Z= 0.182 Angle : 0.667 8.747 14628 Z= 0.362 Chirality : 0.042 0.189 1666 Planarity : 0.004 0.052 1416 Dihedral : 26.362 133.339 2363 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.98 % Favored : 93.80 % Rotamer: Outliers : 3.26 % Allowed : 15.82 % Favored : 80.92 % 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: -1.77 (0.26), residues: 920 helix: 0.09 (0.23), residues: 458 sheet: -1.55 (0.71), residues: 60 loop : -2.68 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 289 TYR 0.016 0.002 TYR E 488 PHE 0.037 0.002 PHE A 345 TRP 0.006 0.001 TRP E 122 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00412 (10440) covalent geometry : angle 0.65941 (14624) hydrogen bonds : bond 0.04318 ( 522) hydrogen bonds : angle 4.35580 ( 1384) metal coordination : bond 0.01672 ( 8) metal coordination : angle 6.29546 ( 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 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.327 Fit side-chains REVERT: A 99 ASN cc_start: 0.7190 (m-40) cc_final: 0.6586 (t0) REVERT: A 304 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 424 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7516 (t) REVERT: A 488 TYR cc_start: 0.5801 (m-10) cc_final: 0.5034 (m-10) REVERT: E 116 LEU cc_start: 0.8431 (mt) cc_final: 0.8087 (mp) REVERT: E 280 MET cc_start: 0.8660 (tpt) cc_final: 0.8276 (tpp) REVERT: E 304 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: E 386 TYR cc_start: 0.5851 (t80) cc_final: 0.5639 (t80) REVERT: E 424 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7358 (t) REVERT: E 426 ILE cc_start: 0.8259 (tt) cc_final: 0.7924 (tt) outliers start: 27 outliers final: 11 residues processed: 112 average time/residue: 0.0867 time to fit residues: 14.4434 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL 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 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 424 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5087 r_free = 0.5087 target = 0.238922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.185241 restraints weight = 13961.472| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 2.31 r_work: 0.4468 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10448 Z= 0.150 Angle : 0.625 7.975 14628 Z= 0.339 Chirality : 0.040 0.190 1666 Planarity : 0.004 0.049 1416 Dihedral : 26.056 131.481 2362 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.78 % Allowed : 18.12 % Favored : 79.11 % 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: 460 sheet: -1.20 (0.73), residues: 60 loop : -2.36 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 309 TYR 0.023 0.002 TYR A 288 PHE 0.013 0.001 PHE A 180 TRP 0.006 0.001 TRP E 122 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00332 (10440) covalent geometry : angle 0.61606 (14624) hydrogen bonds : bond 0.03714 ( 522) hydrogen bonds : angle 4.09172 ( 1384) metal coordination : bond 0.00963 ( 8) metal coordination : angle 6.24190 ( 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 130 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.241 Fit side-chains REVERT: A 99 ASN cc_start: 0.7132 (m-40) cc_final: 0.6554 (t0) REVERT: A 193 GLU cc_start: 0.6687 (tp30) cc_final: 0.6445 (tp30) REVERT: A 304 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: A 424 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7477 (t) REVERT: A 446 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7408 (tm-30) REVERT: E 116 LEU cc_start: 0.8311 (mt) cc_final: 0.7957 (mp) REVERT: E 280 MET cc_start: 0.8670 (tpt) cc_final: 0.8374 (tpt) REVERT: E 424 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7490 (t) REVERT: E 426 ILE cc_start: 0.8223 (tt) cc_final: 0.7907 (tt) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.0873 time to fit residues: 16.0433 Evaluate side-chains 111 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain A residue 261 ILE 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 79 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 377 ILE 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: 0.8980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 42 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.238600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.186219 restraints weight = 13880.654| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 2.38 r_work: 0.4463 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10448 Z= 0.161 Angle : 0.623 8.160 14628 Z= 0.337 Chirality : 0.040 0.157 1666 Planarity : 0.004 0.046 1416 Dihedral : 25.880 130.644 2359 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.50 % Allowed : 18.36 % Favored : 78.14 % 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: -1.02 (0.26), residues: 920 helix: 0.69 (0.24), residues: 446 sheet: -0.84 (0.74), residues: 60 loop : -2.25 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 176 TYR 0.020 0.002 TYR A 288 PHE 0.014 0.002 PHE A 344 TRP 0.004 0.001 TRP A 41 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00360 (10440) covalent geometry : angle 0.61725 (14624) hydrogen bonds : bond 0.03747 ( 522) hydrogen bonds : angle 4.05479 ( 1384) metal coordination : bond 0.01209 ( 8) metal coordination : angle 5.25572 ( 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 130 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.281 Fit side-chains REVERT: A 99 ASN cc_start: 0.7140 (m-40) cc_final: 0.6513 (t0) REVERT: A 221 THR cc_start: 0.8716 (p) cc_final: 0.8418 (m) REVERT: A 280 MET cc_start: 0.8447 (tpt) cc_final: 0.8010 (tpp) REVERT: A 304 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: A 424 VAL cc_start: 0.7778 (OUTLIER) cc_final: 0.7392 (t) REVERT: A 446 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7450 (tm-30) REVERT: E 99 ASN cc_start: 0.7186 (m-40) cc_final: 0.6592 (t0) REVERT: E 116 LEU cc_start: 0.8365 (mt) cc_final: 0.7996 (mp) REVERT: E 221 THR cc_start: 0.8638 (p) cc_final: 0.8318 (m) REVERT: E 280 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8420 (tpt) REVERT: E 424 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7349 (t) REVERT: E 426 ILE cc_start: 0.8270 (tt) cc_final: 0.7944 (tt) REVERT: E 446 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7447 (tm-30) outliers start: 29 outliers final: 22 residues processed: 122 average time/residue: 0.0829 time to fit residues: 15.1730 Evaluate side-chains 123 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 261 ILE 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 380 VAL 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 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 280 MET 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 424 VAL Chi-restraints excluded: chain E residue 468 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN E 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.239169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.186207 restraints weight = 14011.241| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 2.24 r_work: 0.4457 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10448 Z= 0.155 Angle : 0.604 8.105 14628 Z= 0.329 Chirality : 0.040 0.159 1666 Planarity : 0.004 0.046 1416 Dihedral : 25.767 130.034 2359 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.62 % Allowed : 19.57 % Favored : 76.81 % 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: -0.80 (0.27), residues: 920 helix: 0.83 (0.24), residues: 446 sheet: -0.55 (0.78), residues: 60 loop : -2.13 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 176 TYR 0.020 0.002 TYR A 386 PHE 0.015 0.001 PHE A 344 TRP 0.003 0.001 TRP A 41 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00346 (10440) covalent geometry : angle 0.59878 (14624) hydrogen bonds : bond 0.03552 ( 522) hydrogen bonds : angle 3.95759 ( 1384) metal coordination : bond 0.00811 ( 8) metal coordination : angle 5.04609 ( 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 133 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.314 Fit side-chains REVERT: A 99 ASN cc_start: 0.7024 (m-40) cc_final: 0.6430 (t0) REVERT: A 221 THR cc_start: 0.8669 (p) cc_final: 0.8427 (m) REVERT: A 222 MET cc_start: 0.7589 (mtt) cc_final: 0.7373 (mtt) REVERT: A 280 MET cc_start: 0.8438 (tpt) cc_final: 0.7964 (tpp) REVERT: A 304 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: A 424 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7367 (t) REVERT: A 446 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7418 (tm-30) REVERT: E 99 ASN cc_start: 0.7074 (m-40) cc_final: 0.6508 (t0) REVERT: E 116 LEU cc_start: 0.8359 (mt) cc_final: 0.7968 (mp) REVERT: E 221 THR cc_start: 0.8631 (p) cc_final: 0.8382 (m) REVERT: E 280 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8257 (tpt) REVERT: E 424 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7283 (t) REVERT: E 426 ILE cc_start: 0.8239 (tt) cc_final: 0.7927 (tt) REVERT: E 446 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7382 (tm-30) outliers start: 30 outliers final: 22 residues processed: 126 average time/residue: 0.0839 time to fit residues: 15.8932 Evaluate side-chains 123 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 261 ILE 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 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 280 MET 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 424 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.241126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.186480 restraints weight = 14018.774| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 2.30 r_work: 0.4357 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10448 Z= 0.142 Angle : 0.589 7.818 14628 Z= 0.321 Chirality : 0.039 0.169 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.714 130.052 2359 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.50 % Allowed : 20.41 % Favored : 76.09 % 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: -0.69 (0.27), residues: 920 helix: 0.88 (0.24), residues: 448 sheet: -0.45 (0.79), residues: 60 loop : -2.04 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 106 TYR 0.011 0.001 TYR A 288 PHE 0.012 0.001 PHE A 180 TRP 0.003 0.001 TRP E 122 HIS 0.009 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00315 (10440) covalent geometry : angle 0.58347 (14624) hydrogen bonds : bond 0.03423 ( 522) hydrogen bonds : angle 3.87185 ( 1384) metal coordination : bond 0.00567 ( 8) metal coordination : angle 4.72021 ( 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 123 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7037 (m-40) cc_final: 0.6439 (t0) REVERT: A 221 THR cc_start: 0.8690 (p) cc_final: 0.8457 (m) REVERT: A 222 MET cc_start: 0.7674 (mtt) cc_final: 0.7438 (mtt) REVERT: A 280 MET cc_start: 0.8412 (tpt) cc_final: 0.8004 (tpp) REVERT: A 304 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: A 424 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7295 (t) REVERT: A 446 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7394 (tm-30) REVERT: E 99 ASN cc_start: 0.6909 (m-40) cc_final: 0.6488 (t0) REVERT: E 116 LEU cc_start: 0.8312 (mt) cc_final: 0.7937 (mp) REVERT: E 219 MET cc_start: 0.7896 (mtt) cc_final: 0.7690 (mtt) REVERT: E 221 THR cc_start: 0.8632 (p) cc_final: 0.8403 (m) REVERT: E 222 MET cc_start: 0.7624 (mtt) cc_final: 0.7390 (mtt) REVERT: E 280 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (tpt) REVERT: E 424 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7233 (t) REVERT: E 426 ILE cc_start: 0.8246 (tt) cc_final: 0.7951 (tt) REVERT: E 446 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7371 (tm-30) outliers start: 29 outliers final: 21 residues processed: 115 average time/residue: 0.0821 time to fit residues: 14.2471 Evaluate side-chains 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 261 ILE 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 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 280 MET 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 424 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 492 THR 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: 0.9990 chunk 97 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.235779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.181493 restraints weight = 13884.012| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 2.37 r_work: 0.4415 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10448 Z= 0.223 Angle : 0.649 9.734 14628 Z= 0.351 Chirality : 0.042 0.180 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.738 128.775 2359 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.38 % Allowed : 20.29 % Favored : 76.33 % 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: -0.92 (0.27), residues: 920 helix: 0.69 (0.24), residues: 444 sheet: -0.54 (0.80), residues: 60 loop : -2.14 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 477 TYR 0.014 0.002 TYR A 59 PHE 0.016 0.002 PHE A 180 TRP 0.006 0.001 TRP A 122 HIS 0.010 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00516 (10440) covalent geometry : angle 0.64609 (14624) hydrogen bonds : bond 0.04080 ( 522) hydrogen bonds : angle 4.11695 ( 1384) metal coordination : bond 0.01420 ( 8) metal coordination : angle 3.69421 ( 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 122 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7102 (m-40) cc_final: 0.6517 (t0) REVERT: A 280 MET cc_start: 0.8440 (tpt) cc_final: 0.8116 (tpt) REVERT: A 424 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7444 (t) REVERT: A 446 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7455 (tm-30) REVERT: E 116 LEU cc_start: 0.8370 (mt) cc_final: 0.7998 (mp) REVERT: E 219 MET cc_start: 0.7983 (mtt) cc_final: 0.7763 (mtt) REVERT: E 221 THR cc_start: 0.8673 (p) cc_final: 0.8473 (m) REVERT: E 280 MET cc_start: 0.8585 (tpt) cc_final: 0.8238 (tpt) REVERT: E 424 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7476 (t) REVERT: E 426 ILE cc_start: 0.8258 (tt) cc_final: 0.7995 (tt) REVERT: E 446 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 472 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6643 (tp) outliers start: 28 outliers final: 16 residues processed: 116 average time/residue: 0.0898 time to fit residues: 15.4093 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.241714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.187279 restraints weight = 14024.879| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 2.45 r_work: 0.4360 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10448 Z= 0.135 Angle : 0.598 9.159 14628 Z= 0.325 Chirality : 0.039 0.172 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.661 128.850 2356 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.66 % Allowed : 21.62 % Favored : 75.72 % 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: -0.67 (0.27), residues: 920 helix: 0.86 (0.24), residues: 448 sheet: -0.42 (0.79), residues: 58 loop : -1.98 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.011 0.001 TYR A 288 PHE 0.012 0.001 PHE A 344 TRP 0.004 0.001 TRP A 122 HIS 0.008 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00291 (10440) covalent geometry : angle 0.59336 (14624) hydrogen bonds : bond 0.03291 ( 522) hydrogen bonds : angle 3.81826 ( 1384) metal coordination : bond 0.00506 ( 8) metal coordination : angle 4.46358 ( 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 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6923 (m-40) cc_final: 0.6428 (t0) REVERT: A 280 MET cc_start: 0.8458 (tpt) cc_final: 0.8140 (tpt) REVERT: A 446 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7424 (tm-30) REVERT: E 116 LEU cc_start: 0.8269 (mt) cc_final: 0.7890 (mp) REVERT: E 219 MET cc_start: 0.7914 (mtt) cc_final: 0.7711 (mtt) REVERT: E 222 MET cc_start: 0.7702 (mtt) cc_final: 0.7459 (mtt) REVERT: E 280 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8131 (tpt) REVERT: E 424 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7172 (t) REVERT: E 426 ILE cc_start: 0.8277 (tt) cc_final: 0.7990 (tt) REVERT: E 446 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7413 (tm-30) outliers start: 22 outliers final: 12 residues processed: 108 average time/residue: 0.0862 time to fit residues: 13.6612 Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 402 TYR 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 280 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 0.0470 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.243520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.186837 restraints weight = 13913.063| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 2.23 r_work: 0.4530 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10448 Z= 0.133 Angle : 0.583 9.214 14628 Z= 0.317 Chirality : 0.038 0.165 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.647 130.114 2356 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.29 % Allowed : 21.86 % Favored : 75.85 % 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: -0.52 (0.27), residues: 920 helix: 0.98 (0.24), residues: 450 sheet: -0.40 (0.78), residues: 58 loop : -1.91 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.015 0.001 TYR E 386 PHE 0.012 0.001 PHE A 344 TRP 0.004 0.001 TRP E 164 HIS 0.008 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00289 (10440) covalent geometry : angle 0.57930 (14624) hydrogen bonds : bond 0.03199 ( 522) hydrogen bonds : angle 3.69280 ( 1384) metal coordination : bond 0.00520 ( 8) metal coordination : angle 3.84463 ( 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 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.8420 (tpt) cc_final: 0.8084 (tpt) REVERT: A 291 ASP cc_start: 0.6321 (p0) cc_final: 0.6043 (p0) REVERT: A 446 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 116 LEU cc_start: 0.8222 (mt) cc_final: 0.7901 (mp) REVERT: E 280 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8185 (tpt) REVERT: E 426 ILE cc_start: 0.8240 (tt) cc_final: 0.7901 (tt) REVERT: E 446 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7346 (tm-30) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.0843 time to fit residues: 13.3196 Evaluate side-chains 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 402 TYR 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 261 ILE Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 402 TYR Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.242010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.189204 restraints weight = 14109.093| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 2.31 r_work: 0.4373 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10448 Z= 0.145 Angle : 0.589 9.238 14628 Z= 0.320 Chirality : 0.039 0.177 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.609 130.618 2356 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.17 % Allowed : 21.62 % Favored : 76.21 % 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: -0.50 (0.27), residues: 920 helix: 1.02 (0.24), residues: 450 sheet: -0.36 (0.78), residues: 58 loop : -1.93 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 106 TYR 0.016 0.001 TYR A 386 PHE 0.013 0.001 PHE E 180 TRP 0.004 0.001 TRP A 41 HIS 0.008 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00324 (10440) covalent geometry : angle 0.58564 (14624) hydrogen bonds : bond 0.03242 ( 522) hydrogen bonds : angle 3.71918 ( 1384) metal coordination : bond 0.00642 ( 8) metal coordination : angle 3.60262 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.80 seconds wall clock time: 45 minutes 38.61 seconds (2738.61 seconds total)