Starting phenix.real_space_refine on Fri Feb 14 07:03:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqu_20453/02_2025/6pqu_20453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqu_20453/02_2025/6pqu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pqu_20453/02_2025/6pqu_20453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqu_20453/02_2025/6pqu_20453.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqu_20453/02_2025/6pqu_20453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqu_20453/02_2025/6pqu_20453.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'HIS:plan': 1, 'ASP: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: F, E, G, H Time building chain proxies: 7.60, per 1000 atoms: 0.76 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: 2.74 Conformation dependent library (CDL) restraints added in 842.6 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: 4.15 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: 3.79 Time building geometry restraints manager: 3.05 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'E' } 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 31.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- 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 : 0.008 0.060 10440 Z= 0.507 Angle : 0.898 13.413 14624 Z= 0.514 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 : 23.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP E 122 HIS 0.004 0.001 HIS E 483 PHE 0.022 0.003 PHE A 383 TYR 0.014 0.002 TYR E 394 ARG 0.004 0.001 ARG A 276 *********************** 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 : 1.029 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: 0.2186 time to fit residues: 37.2504 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 : 0.931 ------------------------------------------------------------------------------- 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 86 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 20.0000 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.0050 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.5059 r_free = 0.5059 target = 0.235934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.182823 restraints weight = 13750.025| |-----------------------------------------------------------------------------| r_work (start): 0.4657 rms_B_bonded: 2.36 r_work: 0.4453 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10440 Z= 0.216 Angle : 0.694 7.273 14624 Z= 0.383 Chirality : 0.042 0.171 1666 Planarity : 0.005 0.058 1416 Dihedral : 26.681 134.999 2366 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.80 % Favored : 95.98 % Rotamer: Outliers : 2.90 % Allowed : 11.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.24), residues: 920 helix: -0.61 (0.22), residues: 460 sheet: -1.99 (0.66), residues: 60 loop : -3.02 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 122 HIS 0.003 0.001 HIS E 307 PHE 0.013 0.002 PHE A 345 TYR 0.016 0.002 TYR E 488 ARG 0.005 0.000 ARG A 454 *********************** 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 126 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.969 Fit side-chains REVERT: A 116 LEU cc_start: 0.8441 (mt) cc_final: 0.8050 (mp) REVERT: A 179 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 199 ASP cc_start: 0.7598 (m-30) cc_final: 0.7343 (m-30) REVERT: A 236 SER cc_start: 0.1232 (OUTLIER) cc_final: 0.0993 (p) REVERT: A 304 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: E 199 ASP cc_start: 0.7504 (m-30) cc_final: 0.7224 (m-30) REVERT: E 236 SER cc_start: 0.1296 (OUTLIER) cc_final: 0.1055 (p) REVERT: E 291 ASP cc_start: 0.7046 (p0) cc_final: 0.6740 (p0) REVERT: E 304 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7452 (tm-30) outliers start: 24 outliers final: 10 residues processed: 119 average time/residue: 0.2116 time to fit residues: 36.2958 Evaluate side-chains 98 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 404 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.237199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.184016 restraints weight = 13924.876| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 2.42 r_work: 0.4311 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10440 Z= 0.220 Angle : 0.649 7.161 14624 Z= 0.357 Chirality : 0.041 0.195 1666 Planarity : 0.004 0.054 1416 Dihedral : 26.364 133.633 2365 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 3.38 % Allowed : 15.22 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.26), residues: 920 helix: 0.10 (0.24), residues: 458 sheet: -1.42 (0.72), residues: 60 loop : -2.67 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 122 HIS 0.003 0.001 HIS E 413 PHE 0.031 0.002 PHE A 345 TYR 0.018 0.002 TYR E 488 ARG 0.004 0.000 ARG E 289 *********************** 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 124 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.884 Fit side-chains REVERT: A 99 ASN cc_start: 0.7209 (m-40) cc_final: 0.6603 (t0) REVERT: A 148 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7822 (ptm) REVERT: A 260 THR cc_start: 0.1125 (OUTLIER) cc_final: 0.0915 (t) REVERT: A 304 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: A 424 VAL cc_start: 0.7740 (OUTLIER) cc_final: 0.7494 (t) REVERT: A 488 TYR cc_start: 0.5799 (m-10) cc_final: 0.5052 (m-10) REVERT: E 260 THR cc_start: 0.0663 (OUTLIER) cc_final: 0.0446 (t) REVERT: E 280 MET cc_start: 0.8625 (tpt) cc_final: 0.8335 (tpp) REVERT: E 304 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: E 424 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7360 (t) outliers start: 28 outliers final: 12 residues processed: 116 average time/residue: 0.1945 time to fit residues: 33.3491 Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 148 MET Chi-restraints excluded: chain A residue 260 THR 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 260 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.237304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.183331 restraints weight = 13822.211| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 2.31 r_work: 0.4444 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10440 Z= 0.222 Angle : 0.630 7.710 14624 Z= 0.347 Chirality : 0.041 0.196 1666 Planarity : 0.004 0.048 1416 Dihedral : 26.110 132.081 2363 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.14 % Allowed : 17.39 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.26), residues: 920 helix: 0.32 (0.23), residues: 460 sheet: -1.16 (0.73), residues: 60 loop : -2.40 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 122 HIS 0.002 0.001 HIS A 216 PHE 0.014 0.001 PHE A 180 TYR 0.023 0.002 TYR A 288 ARG 0.002 0.000 ARG A 309 *********************** 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 126 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.976 Fit side-chains REVERT: A 99 ASN cc_start: 0.7186 (m-40) cc_final: 0.6567 (t0) REVERT: A 304 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: A 424 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7483 (t) REVERT: A 446 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7437 (tm-30) REVERT: E 280 MET cc_start: 0.8719 (tpt) cc_final: 0.8387 (tpt) REVERT: E 304 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: E 424 VAL cc_start: 0.7778 (OUTLIER) cc_final: 0.7407 (t) outliers start: 26 outliers final: 13 residues processed: 121 average time/residue: 0.2113 time to fit residues: 37.3623 Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.5094 r_free = 0.5094 target = 0.239633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.187068 restraints weight = 13837.526| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 2.36 r_work: 0.4475 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10440 Z= 0.199 Angle : 0.611 7.429 14624 Z= 0.335 Chirality : 0.040 0.159 1666 Planarity : 0.004 0.047 1416 Dihedral : 25.900 131.027 2363 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.86 % Allowed : 18.36 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 920 helix: 0.52 (0.24), residues: 458 sheet: -0.76 (0.74), residues: 60 loop : -2.30 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 122 HIS 0.004 0.001 HIS A 216 PHE 0.012 0.001 PHE A 180 TYR 0.018 0.002 TYR A 288 ARG 0.002 0.000 ARG E 289 *********************** 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 127 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.013 Fit side-chains REVERT: A 99 ASN cc_start: 0.7128 (m-40) cc_final: 0.6537 (t0) REVERT: A 221 THR cc_start: 0.8617 (p) cc_final: 0.8318 (m) REVERT: A 304 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: A 424 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7347 (t) REVERT: A 446 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7400 (tm-30) REVERT: E 99 ASN cc_start: 0.7112 (m-40) cc_final: 0.6518 (t0) REVERT: E 221 THR cc_start: 0.8617 (p) cc_final: 0.8307 (m) REVERT: E 280 MET cc_start: 0.8675 (tpt) cc_final: 0.8420 (tpt) REVERT: E 304 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: E 424 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7412 (t) REVERT: E 446 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7438 (tm-30) outliers start: 32 outliers final: 21 residues processed: 121 average time/residue: 0.1915 time to fit residues: 34.2013 Evaluate side-chains 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 116 LEU 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 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 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 75 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.5073 r_free = 0.5073 target = 0.237454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.184488 restraints weight = 13946.838| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 2.47 r_work: 0.4414 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10440 Z= 0.245 Angle : 0.623 7.850 14624 Z= 0.340 Chirality : 0.041 0.169 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.838 130.270 2362 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.26 % Allowed : 19.20 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.27), residues: 920 helix: 0.65 (0.24), residues: 446 sheet: -0.66 (0.77), residues: 60 loop : -2.20 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 41 HIS 0.007 0.001 HIS E 216 PHE 0.014 0.001 PHE A 180 TYR 0.013 0.002 TYR A 288 ARG 0.003 0.000 ARG A 343 *********************** 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 129 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.922 Fit side-chains REVERT: A 99 ASN cc_start: 0.7137 (m-40) cc_final: 0.6496 (t0) REVERT: A 148 MET cc_start: 0.7806 (ptp) cc_final: 0.7569 (ptp) REVERT: A 221 THR cc_start: 0.8664 (p) cc_final: 0.8389 (m) REVERT: A 280 MET cc_start: 0.8422 (tpt) cc_final: 0.8136 (tpt) REVERT: A 304 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: A 424 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7399 (t) REVERT: A 446 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7479 (tm-30) REVERT: E 99 ASN cc_start: 0.7048 (m-40) cc_final: 0.6479 (t0) REVERT: E 221 THR cc_start: 0.8672 (p) cc_final: 0.8383 (m) REVERT: E 280 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8306 (tpt) REVERT: E 304 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: E 424 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7389 (t) REVERT: E 446 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7442 (tm-30) outliers start: 27 outliers final: 21 residues processed: 122 average time/residue: 0.1871 time to fit residues: 33.7626 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 : 0.775 ------------------------------------------------------------------------------- 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 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 117 ILE 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 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 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 78 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.5097 r_free = 0.5097 target = 0.240022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.186339 restraints weight = 13994.975| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 2.37 r_work: 0.4463 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.194 Angle : 0.595 7.323 14624 Z= 0.326 Chirality : 0.039 0.142 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.739 129.784 2362 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.50 % Allowed : 20.53 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 920 helix: 0.83 (0.24), residues: 448 sheet: -0.50 (0.78), residues: 60 loop : -2.11 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 122 HIS 0.004 0.001 HIS A 216 PHE 0.012 0.001 PHE A 180 TYR 0.010 0.001 TYR E 266 ARG 0.002 0.000 ARG E 176 *********************** 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 128 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.960 Fit side-chains REVERT: A 99 ASN cc_start: 0.7063 (m-40) cc_final: 0.6429 (t0) REVERT: A 216 HIS cc_start: 0.5941 (m-70) cc_final: 0.5707 (m-70) REVERT: A 221 THR cc_start: 0.8651 (p) cc_final: 0.8415 (m) REVERT: A 222 MET cc_start: 0.7703 (mtt) cc_final: 0.7483 (mtt) REVERT: A 304 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: A 424 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7345 (t) REVERT: A 446 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7408 (tm-30) REVERT: E 99 ASN cc_start: 0.6987 (m-40) cc_final: 0.6453 (t0) REVERT: E 219 MET cc_start: 0.7926 (mtt) cc_final: 0.7706 (mtt) REVERT: E 221 THR cc_start: 0.8639 (p) cc_final: 0.8405 (m) REVERT: E 222 MET cc_start: 0.7729 (mtt) cc_final: 0.7507 (mtt) REVERT: E 280 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8399 (tpt) REVERT: E 304 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: E 361 LEU cc_start: 0.6066 (tp) cc_final: 0.5866 (tt) REVERT: E 424 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7327 (t) REVERT: E 446 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7418 (tm-30) outliers start: 29 outliers final: 20 residues processed: 122 average time/residue: 0.1961 time to fit residues: 35.2103 Evaluate side-chains 118 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 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 93 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.5095 r_free = 0.5095 target = 0.240151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.187638 restraints weight = 13952.197| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 2.26 r_work: 0.4464 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10440 Z= 0.200 Angle : 0.595 7.327 14624 Z= 0.326 Chirality : 0.039 0.194 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.689 129.784 2362 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.26 % Allowed : 20.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 920 helix: 0.88 (0.24), residues: 446 sheet: -0.39 (0.78), residues: 60 loop : -2.08 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 41 HIS 0.003 0.001 HIS E 413 PHE 0.019 0.001 PHE A 344 TYR 0.019 0.001 TYR A 386 ARG 0.002 0.000 ARG E 176 *********************** 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 123 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7161 (m-40) cc_final: 0.6527 (t0) REVERT: A 216 HIS cc_start: 0.5940 (m-70) cc_final: 0.5718 (m-70) REVERT: A 221 THR cc_start: 0.8672 (p) cc_final: 0.8469 (m) REVERT: A 222 MET cc_start: 0.7625 (mtt) cc_final: 0.7423 (mtt) REVERT: A 280 MET cc_start: 0.8401 (tpp) cc_final: 0.8043 (tpp) REVERT: A 424 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7099 (t) REVERT: A 446 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7366 (tm-30) REVERT: E 221 THR cc_start: 0.8606 (p) cc_final: 0.8379 (m) REVERT: E 222 MET cc_start: 0.7744 (mtt) cc_final: 0.7528 (mtt) REVERT: E 280 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8269 (tpt) REVERT: E 361 LEU cc_start: 0.6122 (tp) cc_final: 0.5908 (tt) REVERT: E 424 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7400 (t) REVERT: E 446 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7365 (tm-30) outliers start: 27 outliers final: 20 residues processed: 117 average time/residue: 0.2092 time to fit residues: 36.0684 Evaluate side-chains 117 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.5094 r_free = 0.5094 target = 0.240018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.186950 restraints weight = 13970.544| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 2.33 r_work: 0.4461 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10440 Z= 0.205 Angle : 0.593 7.222 14624 Z= 0.325 Chirality : 0.039 0.182 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.641 129.729 2356 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.38 % Allowed : 20.65 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 920 helix: 0.82 (0.24), residues: 446 sheet: -0.37 (0.79), residues: 60 loop : -2.03 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 164 HIS 0.004 0.001 HIS A 413 PHE 0.017 0.001 PHE A 344 TYR 0.014 0.001 TYR E 386 ARG 0.004 0.000 ARG A 100 *********************** 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 126 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7068 (m-40) cc_final: 0.6483 (t0) REVERT: A 216 HIS cc_start: 0.5985 (m-70) cc_final: 0.5778 (m-70) REVERT: A 222 MET cc_start: 0.7655 (mtt) cc_final: 0.7452 (mtt) REVERT: A 280 MET cc_start: 0.8434 (tpp) cc_final: 0.8135 (tpp) REVERT: A 424 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7113 (t) REVERT: A 446 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7385 (tm-30) REVERT: E 222 MET cc_start: 0.7679 (mtt) cc_final: 0.7458 (mtt) REVERT: E 280 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8161 (tpt) REVERT: E 424 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7419 (t) REVERT: E 446 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7404 (tm-30) outliers start: 28 outliers final: 18 residues processed: 120 average time/residue: 0.1969 time to fit residues: 34.7005 Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain A residue 351 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.5101 r_free = 0.5101 target = 0.240789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.185883 restraints weight = 14122.710| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 2.52 r_work: 0.4402 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10440 Z= 0.212 Angle : 0.611 9.482 14624 Z= 0.332 Chirality : 0.040 0.200 1666 Planarity : 0.004 0.043 1416 Dihedral : 25.632 129.722 2356 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.38 % Allowed : 20.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 920 helix: 0.83 (0.24), residues: 446 sheet: -0.53 (0.77), residues: 60 loop : -1.98 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 41 HIS 0.005 0.001 HIS A 413 PHE 0.014 0.001 PHE A 344 TYR 0.015 0.001 TYR A 386 ARG 0.005 0.000 ARG A 100 ********************** 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 122 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6943 (m-40) cc_final: 0.6427 (t0) REVERT: A 216 HIS cc_start: 0.6030 (m-70) cc_final: 0.5792 (m-70) REVERT: A 280 MET cc_start: 0.8364 (tpp) cc_final: 0.8086 (tpp) REVERT: A 446 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7402 (tm-30) REVERT: E 280 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8103 (tpt) REVERT: E 446 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 28 outliers final: 20 residues processed: 115 average time/residue: 0.2030 time to fit residues: 34.4260 Evaluate side-chains 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 205 VAL 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 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 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 468 SER 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 86 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.238735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.184962 restraints weight = 13972.246| |-----------------------------------------------------------------------------| r_work (start): 0.4664 rms_B_bonded: 2.22 r_work: 0.4465 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10440 Z= 0.245 Angle : 0.619 8.932 14624 Z= 0.339 Chirality : 0.041 0.188 1666 Planarity : 0.004 0.042 1416 Dihedral : 25.642 129.293 2356 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 920 helix: 0.75 (0.24), residues: 446 sheet: -0.59 (0.77), residues: 58 loop : -2.03 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 41 HIS 0.004 0.001 HIS A 216 PHE 0.014 0.001 PHE A 180 TYR 0.015 0.001 TYR A 386 ARG 0.004 0.000 ARG E 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4821.62 seconds wall clock time: 86 minutes 23.18 seconds (5183.18 seconds total)