Starting phenix.real_space_refine on Mon Jul 28 01:55:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqu_20453/07_2025/6pqu_20453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqu_20453/07_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_20453/07_2025/6pqu_20453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqu_20453/07_2025/6pqu_20453.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqu_20453/07_2025/6pqu_20453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqu_20453/07_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-5711/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: 8.05, per 1000 atoms: 0.80 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: 2.90 Conformation dependent library (CDL) restraints added in 984.3 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: 4.19 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: 3.99 Time building geometry restraints manager: 3.36 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: 0.05 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: 1.290 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 32.940 Find NCS groups from input model: 0.210 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- 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 : 23.39 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 Details of bonding type rmsd hydrogen bonds : bond 0.15096 ( 522) hydrogen bonds : angle 6.92307 ( 1384) metal coordination : bond 0.06810 ( 8) metal coordination : angle 13.81592 ( 4) covalent geometry : bond 0.00840 (10440) covalent geometry : angle 0.89755 (14624) *********************** 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 : 0.919 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: 0.2143 time to fit residues: 36.7877 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 : 0.907 ------------------------------------------------------------------------------- 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 10448 Z= 0.165 Angle : 0.703 7.895 14628 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 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 522) hydrogen bonds : angle 4.74784 ( 1384) metal coordination : bond 0.01157 ( 8) metal coordination : angle 6.58582 ( 4) covalent geometry : bond 0.00359 (10440) covalent geometry : angle 0.69447 (14624) *********************** 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 : 0.902 Fit side-chains REVERT: A 116 LEU cc_start: 0.8440 (mt) cc_final: 0.8050 (mp) REVERT: A 179 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 199 ASP cc_start: 0.7597 (m-30) cc_final: 0.7341 (m-30) REVERT: A 236 SER cc_start: 0.1229 (OUTLIER) cc_final: 0.0990 (p) REVERT: A 304 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: E 199 ASP cc_start: 0.7503 (m-30) cc_final: 0.7223 (m-30) REVERT: E 236 SER cc_start: 0.1294 (OUTLIER) cc_final: 0.1054 (p) REVERT: E 291 ASP cc_start: 0.7043 (p0) cc_final: 0.6740 (p0) REVERT: E 304 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7451 (tm-30) outliers start: 24 outliers final: 10 residues processed: 119 average time/residue: 0.2952 time to fit residues: 51.4785 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 : 3.331 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.5069 r_free = 0.5069 target = 0.236887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.183423 restraints weight = 13930.153| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 2.30 r_work: 0.4453 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10448 Z= 0.166 Angle : 0.658 8.030 14628 Z= 0.358 Chirality : 0.041 0.203 1666 Planarity : 0.004 0.054 1416 Dihedral : 26.380 133.688 2365 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 3.38 % Allowed : 14.86 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.77 (0.26), residues: 920 helix: 0.07 (0.23), residues: 458 sheet: -1.44 (0.72), residues: 60 loop : -2.68 (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 0.028 0.002 PHE A 345 TYR 0.019 0.002 TYR E 488 ARG 0.005 0.000 ARG E 289 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 522) hydrogen bonds : angle 4.31116 ( 1384) metal coordination : bond 0.01937 ( 8) metal coordination : angle 6.64519 ( 4) covalent geometry : bond 0.00372 (10440) covalent geometry : angle 0.64874 (14624) *********************** 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 : 0.856 Fit side-chains REVERT: A 99 ASN cc_start: 0.7198 (m-40) cc_final: 0.6591 (t0) REVERT: A 304 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: A 424 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7530 (t) REVERT: A 488 TYR cc_start: 0.5742 (m-10) cc_final: 0.4970 (m-10) REVERT: E 116 LEU cc_start: 0.8391 (mt) cc_final: 0.8076 (mp) REVERT: E 148 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7741 (ptm) REVERT: E 260 THR cc_start: 0.0818 (OUTLIER) cc_final: 0.0573 (t) REVERT: E 280 MET cc_start: 0.8672 (tpt) cc_final: 0.8363 (tpp) REVERT: E 291 ASP cc_start: 0.6993 (p0) cc_final: 0.6745 (p0) REVERT: E 304 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: E 424 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7377 (t) outliers start: 28 outliers final: 12 residues processed: 116 average time/residue: 0.1933 time to fit residues: 33.0665 Evaluate side-chains 106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 148 MET 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: 5.9990 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.0040 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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 = 0.5088 r_free = 0.5088 target = 0.238947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.184654 restraints weight = 13844.611| |-----------------------------------------------------------------------------| r_work (start): 0.4664 rms_B_bonded: 2.37 r_work: 0.4467 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10448 Z= 0.151 Angle : 0.625 7.569 14628 Z= 0.340 Chirality : 0.040 0.187 1666 Planarity : 0.004 0.050 1416 Dihedral : 26.041 132.161 2363 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.14 % Allowed : 17.63 % Favored : 79.23 % 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: -1.26 (0.26), residues: 920 helix: 0.40 (0.23), residues: 462 sheet: -1.07 (0.73), residues: 60 loop : -2.34 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 122 HIS 0.003 0.001 HIS A 413 PHE 0.013 0.001 PHE E 180 TYR 0.022 0.002 TYR A 288 ARG 0.003 0.000 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 522) hydrogen bonds : angle 4.08897 ( 1384) metal coordination : bond 0.01076 ( 8) metal coordination : angle 6.51182 ( 4) covalent geometry : bond 0.00333 (10440) covalent geometry : angle 0.61606 (14624) *********************** 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 129 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.967 Fit side-chains REVERT: A 99 ASN cc_start: 0.7199 (m-40) cc_final: 0.6574 (t0) REVERT: A 116 LEU cc_start: 0.8023 (mt) cc_final: 0.7687 (tp) REVERT: A 193 GLU cc_start: 0.6747 (tp30) cc_final: 0.6526 (tp30) REVERT: A 304 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: A 424 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7462 (t) REVERT: A 446 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 280 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8408 (tpt) REVERT: E 424 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7521 (t) outliers start: 26 outliers final: 13 residues processed: 123 average time/residue: 0.2377 time to fit residues: 42.8591 Evaluate side-chains 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 280 MET 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: 0.3980 chunk 92 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.242058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.189443 restraints weight = 13884.513| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 2.45 r_work: 0.4440 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10448 Z= 0.135 Angle : 0.606 7.021 14628 Z= 0.328 Chirality : 0.039 0.167 1666 Planarity : 0.004 0.047 1416 Dihedral : 25.822 132.027 2360 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.14 % Allowed : 18.36 % Favored : 78.50 % 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: -0.88 (0.27), residues: 920 helix: 0.77 (0.24), residues: 448 sheet: -0.67 (0.74), residues: 60 loop : -2.19 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 122 HIS 0.007 0.001 HIS A 216 PHE 0.013 0.001 PHE E 180 TYR 0.020 0.001 TYR A 288 ARG 0.002 0.000 ARG E 289 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 522) hydrogen bonds : angle 3.92213 ( 1384) metal coordination : bond 0.00788 ( 8) metal coordination : angle 5.76613 ( 4) covalent geometry : bond 0.00291 (10440) covalent geometry : angle 0.59851 (14624) *********************** 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 123 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.949 Fit side-chains REVERT: A 99 ASN cc_start: 0.7020 (m-40) cc_final: 0.6383 (t0) REVERT: A 304 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: A 424 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7258 (t) REVERT: A 446 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 280 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8214 (tpt) REVERT: E 424 VAL cc_start: 0.7565 (OUTLIER) cc_final: 0.7322 (t) outliers start: 26 outliers final: 15 residues processed: 115 average time/residue: 0.1931 time to fit residues: 33.0966 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 : 0.985 ------------------------------------------------------------------------------- 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 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 380 VAL Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 424 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 overall best weight: 2.1804 ------------------------------------------------------------------------------- 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 = 0.5047 r_free = 0.5047 target = 0.234508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.179213 restraints weight = 13893.431| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 2.32 r_work: 0.4401 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10448 Z= 0.240 Angle : 0.675 8.577 14628 Z= 0.365 Chirality : 0.043 0.182 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.864 130.739 2359 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.02 % Allowed : 19.57 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.13 (0.26), residues: 920 helix: 0.55 (0.24), residues: 444 sheet: -0.75 (0.76), residues: 60 loop : -2.27 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 122 HIS 0.009 0.001 HIS A 216 PHE 0.015 0.002 PHE A 180 TYR 0.018 0.002 TYR A 288 ARG 0.002 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 522) hydrogen bonds : angle 4.25406 ( 1384) metal coordination : bond 0.01725 ( 8) metal coordination : angle 4.34801 ( 4) covalent geometry : bond 0.00557 (10440) covalent geometry : angle 0.67162 (14624) *********************** 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 120 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.137 Fit side-chains REVERT: A 99 ASN cc_start: 0.7095 (m-40) cc_final: 0.6528 (t0) REVERT: A 221 THR cc_start: 0.8700 (p) cc_final: 0.8440 (m) REVERT: A 280 MET cc_start: 0.8524 (tpt) cc_final: 0.8263 (tpt) REVERT: A 304 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: A 424 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7448 (t) REVERT: A 446 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7495 (tm-30) REVERT: E 99 ASN cc_start: 0.7081 (m-40) cc_final: 0.6521 (t0) REVERT: E 221 THR cc_start: 0.8679 (p) cc_final: 0.8445 (m) REVERT: E 280 MET cc_start: 0.8608 (tpt) cc_final: 0.8268 (tpt) REVERT: E 424 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7490 (t) REVERT: E 446 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7470 (tm-30) outliers start: 25 outliers final: 16 residues processed: 117 average time/residue: 0.2738 time to fit residues: 47.9782 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 : 2.224 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.5094 r_free = 0.5094 target = 0.239963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.184659 restraints weight = 13999.215| |-----------------------------------------------------------------------------| r_work (start): 0.4657 rms_B_bonded: 2.32 r_work: 0.4449 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3143 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= 0.143 Angle : 0.611 7.192 14628 Z= 0.330 Chirality : 0.039 0.148 1666 Planarity : 0.004 0.046 1416 Dihedral : 25.735 130.090 2359 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.90 % Allowed : 20.65 % Favored : 76.45 % 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: -0.80 (0.27), residues: 920 helix: 0.80 (0.24), residues: 448 sheet: -0.60 (0.78), residues: 60 loop : -2.10 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 122 HIS 0.004 0.001 HIS A 413 PHE 0.011 0.001 PHE E 180 TYR 0.013 0.001 TYR A 288 ARG 0.002 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 522) hydrogen bonds : angle 3.95235 ( 1384) metal coordination : bond 0.00601 ( 8) metal coordination : angle 5.00515 ( 4) covalent geometry : bond 0.00315 (10440) covalent geometry : angle 0.60562 (14624) *********************** 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 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.889 Fit side-chains REVERT: A 99 ASN cc_start: 0.6966 (m-40) cc_final: 0.6481 (t0) REVERT: A 216 HIS cc_start: 0.6075 (m-70) cc_final: 0.5788 (m-70) REVERT: A 221 THR cc_start: 0.8644 (p) cc_final: 0.8414 (m) REVERT: A 280 MET cc_start: 0.8541 (tpt) cc_final: 0.8245 (tpp) REVERT: A 304 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: A 424 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7353 (t) REVERT: A 446 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7416 (tm-30) REVERT: E 280 MET cc_start: 0.8477 (tpt) cc_final: 0.8187 (tpt) REVERT: E 424 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7350 (t) REVERT: E 446 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7393 (tm-30) outliers start: 24 outliers final: 19 residues processed: 112 average time/residue: 0.1922 time to fit residues: 32.0519 Evaluate side-chains 111 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 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 162 THR Chi-restraints excluded: chain E residue 233 GLU 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 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 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: 0.7980 chunk 9 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.5098 r_free = 0.5098 target = 0.240433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.185748 restraints weight = 13909.710| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 2.42 r_work: 0.4458 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3312 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= 0.148 Angle : 0.604 7.642 14628 Z= 0.328 Chirality : 0.039 0.147 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.689 130.075 2359 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -0.69 (0.27), residues: 920 helix: 0.91 (0.24), residues: 448 sheet: -0.59 (0.78), residues: 60 loop : -2.05 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 41 HIS 0.004 0.001 HIS E 216 PHE 0.013 0.001 PHE A 344 TYR 0.016 0.001 TYR E 386 ARG 0.003 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 522) hydrogen bonds : angle 3.88544 ( 1384) metal coordination : bond 0.00872 ( 8) metal coordination : angle 4.25637 ( 4) covalent geometry : bond 0.00329 (10440) covalent geometry : angle 0.60011 (14624) *********************** 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 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 280 MET cc_start: 0.8588 (tpt) cc_final: 0.8322 (tpp) REVERT: A 424 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7462 (t) REVERT: A 446 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7392 (tm-30) REVERT: E 280 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8135 (tpt) REVERT: E 361 LEU cc_start: 0.6416 (tp) cc_final: 0.6122 (tt) REVERT: E 446 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7373 (tm-30) outliers start: 27 outliers final: 20 residues processed: 114 average time/residue: 0.1897 time to fit residues: 32.2131 Evaluate side-chains 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.5100 r_free = 0.5100 target = 0.240876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.183250 restraints weight = 14010.657| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 2.25 r_work: 0.4472 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10448 Z= 0.151 Angle : 0.606 8.863 14628 Z= 0.328 Chirality : 0.039 0.169 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.643 129.967 2356 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.02 % Allowed : 21.50 % 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: -0.68 (0.27), residues: 920 helix: 0.92 (0.24), residues: 446 sheet: -0.73 (0.75), residues: 60 loop : -2.02 (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 0.014 0.001 PHE A 344 TYR 0.014 0.001 TYR A 288 ARG 0.005 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 522) hydrogen bonds : angle 3.85294 ( 1384) metal coordination : bond 0.00720 ( 8) metal coordination : angle 4.04833 ( 4) covalent geometry : bond 0.00337 (10440) covalent geometry : angle 0.60201 (14624) *********************** 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 117 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 THR cc_start: 0.8608 (p) cc_final: 0.8402 (m) REVERT: A 280 MET cc_start: 0.8578 (tpt) cc_final: 0.8279 (tpp) REVERT: A 424 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7223 (t) REVERT: A 446 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7357 (tm-30) REVERT: E 280 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8159 (tpt) REVERT: E 361 LEU cc_start: 0.6381 (tp) cc_final: 0.6133 (tt) REVERT: E 446 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7395 (tm-30) outliers start: 25 outliers final: 19 residues processed: 112 average time/residue: 0.1928 time to fit residues: 32.1008 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 : 0.935 ------------------------------------------------------------------------------- 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 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 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 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 89 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.246971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.187097 restraints weight = 14387.819| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 2.46 r_work: 0.4422 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10448 Z= 0.187 Angle : 0.632 9.170 14628 Z= 0.342 Chirality : 0.041 0.211 1666 Planarity : 0.004 0.044 1416 Dihedral : 25.656 129.357 2356 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.02 % Allowed : 21.26 % 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 (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: -0.79 (0.27), residues: 920 helix: 0.74 (0.24), residues: 448 sheet: -0.88 (0.75), residues: 60 loop : -1.96 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 41 HIS 0.005 0.001 HIS E 216 PHE 0.015 0.001 PHE E 180 TYR 0.014 0.001 TYR E 386 ARG 0.005 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 522) hydrogen bonds : angle 3.96865 ( 1384) metal coordination : bond 0.01072 ( 8) metal coordination : angle 3.44747 ( 4) covalent geometry : bond 0.00429 (10440) covalent geometry : angle 0.62950 (14624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 280 MET cc_start: 0.8583 (tpt) cc_final: 0.8346 (tpp) REVERT: A 424 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7317 (t) REVERT: A 446 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7497 (tm-30) REVERT: E 280 MET cc_start: 0.8483 (tpt) cc_final: 0.8178 (tpt) REVERT: E 291 ASP cc_start: 0.6908 (p0) cc_final: 0.6535 (p0) REVERT: E 361 LEU cc_start: 0.6488 (tp) cc_final: 0.6136 (tt) REVERT: E 446 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7486 (tm-30) outliers start: 25 outliers final: 19 residues processed: 108 average time/residue: 0.1894 time to fit residues: 30.4417 Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 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 148 MET 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 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: 0.9980 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 0.0010 chunk 11 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.251131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.192165 restraints weight = 14373.247| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 2.46 r_work: 0.4477 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3650 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= 0.141 Angle : 0.600 8.880 14628 Z= 0.326 Chirality : 0.039 0.193 1666 Planarity : 0.004 0.045 1416 Dihedral : 25.624 129.524 2356 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.78 % Allowed : 21.86 % Favored : 75.36 % 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: -0.62 (0.27), residues: 920 helix: 0.91 (0.24), residues: 448 sheet: -0.67 (0.76), residues: 58 loop : -1.93 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 164 HIS 0.004 0.001 HIS A 216 PHE 0.012 0.001 PHE E 180 TYR 0.016 0.001 TYR E 386 ARG 0.005 0.000 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 522) hydrogen bonds : angle 3.83126 ( 1384) metal coordination : bond 0.00650 ( 8) metal coordination : angle 3.77984 ( 4) covalent geometry : bond 0.00311 (10440) covalent geometry : angle 0.59709 (14624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5558.57 seconds wall clock time: 98 minutes 32.19 seconds (5912.19 seconds total)