Starting phenix.real_space_refine on Wed Mar 4 02:14:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pr5_20457/03_2026/6pr5_20457.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pr5_20457/03_2026/6pr5_20457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pr5_20457/03_2026/6pr5_20457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pr5_20457/03_2026/6pr5_20457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pr5_20457/03_2026/6pr5_20457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pr5_20457/03_2026/6pr5_20457.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 124 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 6073 2.51 5 N 1773 2.21 5 O 2182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10194 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 324 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 181 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 755 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1720 SG CYS A 240 28.075 20.995 56.182 1.00 66.94 S ATOM 1746 SG CYS A 243 26.675 18.929 53.984 1.00 66.43 S ATOM 5543 SG CYS E 240 66.736 74.745 53.312 1.00 75.78 S ATOM 5569 SG CYS E 243 68.439 75.903 50.736 1.00 75.72 S Time building chain proxies: 2.12, per 1000 atoms: 0.21 Number of scatterers: 10194 At special positions: 0 Unit cell: (97.65, 101.85, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 36 16.00 P 124 15.00 Mg 4 11.99 O 2182 8.00 N 1773 7.00 C 6073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 384.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 240 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 408 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 413 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 243 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 240 " Number of angles added : 4 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 53.3% alpha, 15.0% beta 60 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.535A pdb=" N GLU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.802A pdb=" N ILE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 271 through 289 removed outlier: 3.737A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 289 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.536A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.572A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (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 413 through 421 removed outlier: 3.764A pdb=" N ASN A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.583A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.749A pdb=" N THR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 39 through 52 Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 186 through 203 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.796A pdb=" N SER E 251 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 271 through 289 removed outlier: 3.675A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 322 Processing helix chain 'E' and resid 337 through 347 removed outlier: 4.653A pdb=" N PHE E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 413 through 421 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.808A pdb=" N LYS E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS E 447 " --> pdb=" O ARG E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 469 Processing helix chain 'E' and resid 470 through 476 removed outlier: 3.665A pdb=" N THR E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 164 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 158 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE A 147 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA A 127 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR A 149 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 125 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 116 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS A 217 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 118 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET A 219 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 120 " --> pdb=" O MET A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.128A pdb=" N ILE A 377 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP E 164 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA E 158 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 119 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU E 156 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 117 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU E 116 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS E 217 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 118 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET E 219 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER E 120 " --> pdb=" O MET E 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 328 through 329 Processing sheet with id=AA7, first strand: chain 'E' and resid 377 through 378 removed outlier: 4.145A pdb=" N ILE E 377 " --> pdb=" O GLN E 497 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 298 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.08 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: 2124 1.33 - 1.45: 2836 1.45 - 1.57: 5380 1.57 - 1.69: 242 1.69 - 1.81: 56 Bond restraints: 10638 Sorted by residual: bond pdb=" C TYR A 73 " pdb=" N PRO A 74 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N GLN A 330 " pdb=" CA GLN A 330 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N CYS A 72 " pdb=" CA CYS A 72 " ideal model delta sigma weight residual 1.457 1.424 0.032 1.32e-02 5.74e+03 6.00e+00 bond pdb=" CB VAL A 152 " pdb=" CG1 VAL A 152 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL E 152 " pdb=" CG1 VAL E 152 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.62e+00 ... (remaining 10633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14508 2.11 - 4.21: 347 4.21 - 6.32: 25 6.32 - 8.43: 9 8.43 - 10.53: 3 Bond angle restraints: 14892 Sorted by residual: angle pdb=" O3' DT F 2 " pdb=" C3' DT F 2 " pdb=" C2' DT F 2 " ideal model delta sigma weight residual 111.50 102.43 9.07 1.50e+00 4.44e-01 3.66e+01 angle pdb=" C ASP E 379 " pdb=" N VAL E 380 " pdb=" CA VAL E 380 " ideal model delta sigma weight residual 120.24 123.50 -3.26 6.30e-01 2.52e+00 2.68e+01 angle pdb=" O3' DG H 31 " pdb=" C3' DG H 31 " pdb=" C2' DG H 31 " ideal model delta sigma weight residual 111.50 104.64 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DG B 12 " pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 111.50 105.18 6.32 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N GLU E 138 " pdb=" CA GLU E 138 " pdb=" C GLU E 138 " ideal model delta sigma weight residual 110.80 119.50 -8.70 2.13e+00 2.20e-01 1.67e+01 ... (remaining 14887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 5430 32.04 - 64.08: 673 64.08 - 96.12: 24 96.12 - 128.15: 1 128.15 - 160.19: 2 Dihedral angle restraints: 6130 sinusoidal: 3302 harmonic: 2828 Sorted by residual: dihedral pdb=" CA GLY E 427 " pdb=" C GLY E 427 " pdb=" N SER E 428 " pdb=" CA SER E 428 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLY A 427 " pdb=" C GLY A 427 " pdb=" N SER A 428 " pdb=" CA SER A 428 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU A 138 " pdb=" C GLU A 138 " pdb=" N SER A 139 " pdb=" CA SER A 139 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 6127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1369 0.058 - 0.117: 285 0.117 - 0.175: 31 0.175 - 0.233: 3 0.233 - 0.291: 2 Chirality restraints: 1690 Sorted by residual: chirality pdb=" CA GLU E 138 " pdb=" N GLU E 138 " pdb=" C GLU E 138 " pdb=" CB GLU E 138 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB THR E 334 " pdb=" CA THR E 334 " pdb=" OG1 THR E 334 " pdb=" CG2 THR E 334 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA CYS A 72 " pdb=" N CYS A 72 " pdb=" C CYS A 72 " pdb=" CB CYS A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1687 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT F 2 " -0.008 2.00e-02 2.50e+03 1.57e-02 6.19e+00 pdb=" N1 DT F 2 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DT F 2 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT F 2 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT F 2 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DT F 2 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT F 2 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT F 2 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 11 " -0.027 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 DA D 11 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA D 11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA D 11 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA D 11 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA D 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA D 11 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA D 11 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 16 " -0.001 2.00e-02 2.50e+03 1.49e-02 5.55e+00 pdb=" N1 DT B 16 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DT B 16 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT B 16 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT B 16 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT B 16 " -0.034 2.00e-02 2.50e+03 pdb=" C7 DT B 16 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT B 16 " 0.026 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 95 2.55 - 3.14: 8049 3.14 - 3.73: 17032 3.73 - 4.31: 23758 4.31 - 4.90: 37759 Nonbonded interactions: 86693 Sorted by model distance: nonbonded pdb=" O3' DC F 9 " pdb="MG MG E 601 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASP E 125 " pdb="MG MG E 601 " model vdw 2.123 2.170 nonbonded pdb=" OD2 ASP E 125 " pdb="MG MG E 602 " model vdw 2.133 2.170 nonbonded pdb=" OD2 ASP E 224 " pdb="MG MG E 601 " model vdw 2.138 2.170 nonbonded pdb=" OE1 GLU E 435 " pdb="MG MG E 602 " model vdw 2.149 2.170 ... (remaining 86688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 1.590 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.010 0.425 10646 Z= 0.399 Angle : 0.845 30.834 14896 Z= 0.452 Chirality : 0.047 0.291 1690 Planarity : 0.004 0.039 1452 Dihedral : 22.941 160.193 4294 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.36 % Favored : 98.33 % Rotamer: Outliers : 0.71 % Allowed : 10.47 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.21), residues: 956 helix: -1.83 (0.19), residues: 506 sheet: -1.05 (0.60), residues: 64 loop : -2.71 (0.23), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 477 TYR 0.012 0.002 TYR E 394 PHE 0.015 0.002 PHE A 292 TRP 0.017 0.002 TRP A 41 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00802 (10638) covalent geometry : angle 0.77552 (14892) hydrogen bonds : bond 0.11626 ( 520) hydrogen bonds : angle 6.07128 ( 1411) metal coordination : bond 0.19508 ( 8) metal coordination : angle 20.53761 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8418 (p0) cc_final: 0.8170 (p0) REVERT: A 212 HIS cc_start: 0.7804 (m90) cc_final: 0.7395 (m170) REVERT: E 173 MET cc_start: 0.7294 (mtp) cc_final: 0.6998 (mtp) REVERT: E 184 LYS cc_start: 0.8311 (tttt) cc_final: 0.7833 (tppt) REVERT: E 295 TRP cc_start: 0.8549 (t60) cc_final: 0.8314 (t-100) REVERT: E 423 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8101 (tt) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.1102 time to fit residues: 17.6708 Evaluate side-chains 80 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS A 339 ASN A 448 HIS A 486 GLN E 71 GLN E 91 GLN E 130 GLN E 136 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS E 322 ASN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111403 restraints weight = 16183.879| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.00 r_work: 0.3366 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10646 Z= 0.175 Angle : 0.627 11.940 14896 Z= 0.344 Chirality : 0.039 0.182 1690 Planarity : 0.004 0.040 1452 Dihedral : 26.049 159.855 2392 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.03 % Favored : 96.86 % Rotamer: Outliers : 2.12 % Allowed : 13.41 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.25), residues: 956 helix: -0.07 (0.22), residues: 500 sheet: -1.03 (0.59), residues: 64 loop : -2.14 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 437 TYR 0.014 0.001 TYR E 241 PHE 0.013 0.002 PHE A 124 TRP 0.017 0.001 TRP A 41 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00399 (10638) covalent geometry : angle 0.62617 (14892) hydrogen bonds : bond 0.04331 ( 520) hydrogen bonds : angle 4.57701 ( 1411) metal coordination : bond 0.01110 ( 8) metal coordination : angle 2.33633 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 145 SER cc_start: 0.8918 (p) cc_final: 0.8666 (m) REVERT: E 106 ARG cc_start: 0.8028 (mmt180) cc_final: 0.7714 (mmt180) REVERT: E 173 MET cc_start: 0.8048 (mtp) cc_final: 0.7677 (mtp) REVERT: E 184 LYS cc_start: 0.8552 (tttt) cc_final: 0.7696 (tppt) REVERT: E 307 HIS cc_start: 0.8275 (m90) cc_final: 0.7945 (m90) REVERT: E 336 ASN cc_start: 0.8408 (m-40) cc_final: 0.8176 (m-40) REVERT: E 423 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8268 (tt) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.0957 time to fit residues: 14.9322 Evaluate side-chains 92 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 14 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 129 ASN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.140467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114293 restraints weight = 16245.485| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.01 r_work: 0.3410 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10646 Z= 0.144 Angle : 0.561 8.202 14896 Z= 0.315 Chirality : 0.037 0.181 1690 Planarity : 0.004 0.042 1452 Dihedral : 25.920 163.675 2391 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 1.88 % Allowed : 17.29 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.27), residues: 956 helix: 0.95 (0.24), residues: 500 sheet: -0.91 (0.58), residues: 64 loop : -1.80 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 437 TYR 0.013 0.001 TYR E 241 PHE 0.013 0.001 PHE A 292 TRP 0.014 0.001 TRP A 41 HIS 0.002 0.001 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00318 (10638) covalent geometry : angle 0.56011 (14892) hydrogen bonds : bond 0.03670 ( 520) hydrogen bonds : angle 4.11882 ( 1411) metal coordination : bond 0.00530 ( 8) metal coordination : angle 1.62939 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.278 Fit side-chains REVERT: A 145 SER cc_start: 0.8773 (p) cc_final: 0.8335 (m) REVERT: A 199 ASP cc_start: 0.8326 (t0) cc_final: 0.7963 (m-30) REVERT: A 219 MET cc_start: 0.8941 (ptm) cc_final: 0.8699 (ptm) REVERT: A 315 ASP cc_start: 0.8065 (m-30) cc_final: 0.7742 (m-30) REVERT: E 173 MET cc_start: 0.7858 (mtp) cc_final: 0.7525 (mtp) REVERT: E 179 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8418 (pp30) REVERT: E 184 LYS cc_start: 0.8405 (tttt) cc_final: 0.7544 (tppt) REVERT: E 307 HIS cc_start: 0.8249 (m90) cc_final: 0.8002 (m90) REVERT: E 423 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8329 (tt) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.0960 time to fit residues: 15.5917 Evaluate side-chains 96 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.139393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113010 restraints weight = 16284.717| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.00 r_work: 0.3393 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10646 Z= 0.172 Angle : 0.574 9.061 14896 Z= 0.319 Chirality : 0.038 0.211 1690 Planarity : 0.004 0.038 1452 Dihedral : 25.950 164.886 2391 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 2.47 % Allowed : 18.12 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 956 helix: 1.26 (0.24), residues: 500 sheet: -0.75 (0.59), residues: 64 loop : -1.69 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 437 TYR 0.012 0.001 TYR A 62 PHE 0.012 0.001 PHE E 180 TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00390 (10638) covalent geometry : angle 0.57356 (14892) hydrogen bonds : bond 0.03855 ( 520) hydrogen bonds : angle 4.08207 ( 1411) metal coordination : bond 0.00680 ( 8) metal coordination : angle 1.87772 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.349 Fit side-chains REVERT: A 124 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8848 (p90) REVERT: A 145 SER cc_start: 0.8849 (p) cc_final: 0.8341 (m) REVERT: A 219 MET cc_start: 0.9002 (ptm) cc_final: 0.8753 (ptm) REVERT: A 315 ASP cc_start: 0.8148 (m-30) cc_final: 0.7776 (m-30) REVERT: E 173 MET cc_start: 0.7858 (mtp) cc_final: 0.7499 (mtp) REVERT: E 179 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8561 (pp30) REVERT: E 184 LYS cc_start: 0.8443 (tttt) cc_final: 0.7580 (tppt) REVERT: E 423 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8077 (tt) REVERT: E 470 ASP cc_start: 0.8412 (t70) cc_final: 0.8145 (t0) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.0894 time to fit residues: 13.6744 Evaluate side-chains 96 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** 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 = 0.3851 r_free = 0.3851 target = 0.139410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113686 restraints weight = 16033.372| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.90 r_work: 0.3398 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10646 Z= 0.160 Angle : 0.568 8.816 14896 Z= 0.316 Chirality : 0.038 0.222 1690 Planarity : 0.004 0.038 1452 Dihedral : 25.909 165.115 2391 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 2.24 % Allowed : 18.94 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 956 helix: 1.33 (0.24), residues: 516 sheet: -0.64 (0.59), residues: 64 loop : -1.66 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 106 TYR 0.011 0.001 TYR A 62 PHE 0.014 0.001 PHE A 292 TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00361 (10638) covalent geometry : angle 0.56697 (14892) hydrogen bonds : bond 0.03817 ( 520) hydrogen bonds : angle 4.03825 ( 1411) metal coordination : bond 0.00538 ( 8) metal coordination : angle 1.82590 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.365 Fit side-chains REVERT: A 124 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8727 (p90) REVERT: E 173 MET cc_start: 0.8126 (mtp) cc_final: 0.7765 (mtp) REVERT: E 184 LYS cc_start: 0.8553 (tttt) cc_final: 0.7703 (tppt) REVERT: E 423 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8012 (tt) REVERT: E 470 ASP cc_start: 0.8358 (t70) cc_final: 0.8077 (t0) outliers start: 19 outliers final: 15 residues processed: 102 average time/residue: 0.0876 time to fit residues: 13.5477 Evaluate side-chains 90 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110721 restraints weight = 16367.530| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.06 r_work: 0.3371 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10646 Z= 0.178 Angle : 0.579 8.940 14896 Z= 0.319 Chirality : 0.039 0.230 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.932 165.513 2391 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.98 % Rotamer: Outliers : 2.59 % Allowed : 19.18 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 956 helix: 1.49 (0.24), residues: 502 sheet: -0.59 (0.59), residues: 64 loop : -1.66 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 52 TYR 0.012 0.001 TYR A 62 PHE 0.011 0.001 PHE A 180 TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00405 (10638) covalent geometry : angle 0.57774 (14892) hydrogen bonds : bond 0.03930 ( 520) hydrogen bonds : angle 4.02937 ( 1411) metal coordination : bond 0.00696 ( 8) metal coordination : angle 1.97027 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8755 (p90) REVERT: E 173 MET cc_start: 0.7934 (mtp) cc_final: 0.7592 (mtp) REVERT: E 184 LYS cc_start: 0.8450 (tttt) cc_final: 0.7603 (tppt) REVERT: E 470 ASP cc_start: 0.8233 (t70) cc_final: 0.7887 (t0) outliers start: 22 outliers final: 20 residues processed: 92 average time/residue: 0.0817 time to fit residues: 11.5754 Evaluate side-chains 93 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.0000 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114419 restraints weight = 15987.706| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.99 r_work: 0.3419 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10646 Z= 0.139 Angle : 0.541 9.030 14896 Z= 0.303 Chirality : 0.037 0.218 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.816 165.643 2389 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.59 % Allowed : 19.53 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.28), residues: 956 helix: 1.61 (0.24), residues: 516 sheet: -0.58 (0.59), residues: 64 loop : -1.55 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 52 TYR 0.015 0.001 TYR E 241 PHE 0.016 0.001 PHE A 292 TRP 0.013 0.001 TRP A 41 HIS 0.002 0.000 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00311 (10638) covalent geometry : angle 0.54062 (14892) hydrogen bonds : bond 0.03655 ( 520) hydrogen bonds : angle 3.93058 ( 1411) metal coordination : bond 0.00310 ( 8) metal coordination : angle 1.53842 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.323 Fit side-chains REVERT: A 124 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8604 (p90) REVERT: A 145 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8415 (m) REVERT: A 337 ASP cc_start: 0.7648 (m-30) cc_final: 0.7384 (m-30) REVERT: E 173 MET cc_start: 0.7894 (mtp) cc_final: 0.7545 (mtp) REVERT: E 184 LYS cc_start: 0.8447 (tttt) cc_final: 0.7583 (tppt) REVERT: E 410 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8105 (mm) REVERT: E 470 ASP cc_start: 0.8091 (t70) cc_final: 0.7881 (t0) outliers start: 22 outliers final: 19 residues processed: 103 average time/residue: 0.0752 time to fit residues: 12.0911 Evaluate side-chains 102 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** 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 = 0.3892 r_free = 0.3892 target = 0.142651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116467 restraints weight = 15931.404| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.98 r_work: 0.3446 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10646 Z= 0.130 Angle : 0.538 8.959 14896 Z= 0.301 Chirality : 0.036 0.234 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.666 166.648 2389 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.47 % Allowed : 20.00 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.28), residues: 956 helix: 1.77 (0.24), residues: 516 sheet: -0.48 (0.59), residues: 64 loop : -1.53 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 52 TYR 0.015 0.001 TYR E 241 PHE 0.010 0.001 PHE A 180 TRP 0.012 0.001 TRP A 41 HIS 0.002 0.000 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00284 (10638) covalent geometry : angle 0.53741 (14892) hydrogen bonds : bond 0.03556 ( 520) hydrogen bonds : angle 3.82369 ( 1411) metal coordination : bond 0.00278 ( 8) metal coordination : angle 1.25042 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.284 Fit side-chains REVERT: A 124 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8408 (p90) REVERT: A 145 SER cc_start: 0.8718 (p) cc_final: 0.8361 (m) REVERT: A 337 ASP cc_start: 0.7632 (m-30) cc_final: 0.7420 (m-30) REVERT: E 173 MET cc_start: 0.7773 (mtp) cc_final: 0.7418 (mtp) REVERT: E 184 LYS cc_start: 0.8573 (tttt) cc_final: 0.7756 (tppt) outliers start: 21 outliers final: 19 residues processed: 112 average time/residue: 0.0747 time to fit residues: 13.1178 Evaluate side-chains 101 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113495 restraints weight = 15990.536| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.96 r_work: 0.3406 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10646 Z= 0.172 Angle : 0.581 9.519 14896 Z= 0.321 Chirality : 0.038 0.246 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.790 167.760 2389 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.82 % Allowed : 20.47 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.27), residues: 956 helix: 1.64 (0.24), residues: 516 sheet: -0.51 (0.58), residues: 64 loop : -1.52 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 52 TYR 0.012 0.001 TYR E 241 PHE 0.013 0.001 PHE A 292 TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00391 (10638) covalent geometry : angle 0.58077 (14892) hydrogen bonds : bond 0.03919 ( 520) hydrogen bonds : angle 3.94686 ( 1411) metal coordination : bond 0.00571 ( 8) metal coordination : angle 1.27443 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.344 Fit side-chains REVERT: A 124 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8660 (p90) REVERT: A 337 ASP cc_start: 0.7807 (m-30) cc_final: 0.7583 (m-30) REVERT: E 173 MET cc_start: 0.8088 (mtp) cc_final: 0.7710 (mtp) REVERT: E 184 LYS cc_start: 0.8676 (tttt) cc_final: 0.7811 (tppt) REVERT: E 410 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (mm) outliers start: 24 outliers final: 22 residues processed: 98 average time/residue: 0.0814 time to fit residues: 12.1025 Evaluate side-chains 99 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** 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 = 0.3871 r_free = 0.3871 target = 0.140786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114599 restraints weight = 15852.764| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.96 r_work: 0.3392 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10646 Z= 0.152 Angle : 0.577 10.513 14896 Z= 0.322 Chirality : 0.038 0.245 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.761 167.426 2389 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.82 % Allowed : 20.71 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.28), residues: 956 helix: 1.60 (0.24), residues: 518 sheet: -0.49 (0.59), residues: 64 loop : -1.47 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 176 TYR 0.023 0.001 TYR E 241 PHE 0.013 0.001 PHE A 344 TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00341 (10638) covalent geometry : angle 0.57718 (14892) hydrogen bonds : bond 0.03857 ( 520) hydrogen bonds : angle 3.92563 ( 1411) metal coordination : bond 0.00457 ( 8) metal coordination : angle 1.17313 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.336 Fit side-chains REVERT: A 124 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8588 (p90) REVERT: A 212 HIS cc_start: 0.8397 (m90) cc_final: 0.7944 (m170) REVERT: A 337 ASP cc_start: 0.7788 (m-30) cc_final: 0.7560 (m-30) REVERT: E 173 MET cc_start: 0.7809 (mtp) cc_final: 0.7460 (mtp) REVERT: E 184 LYS cc_start: 0.8600 (tttt) cc_final: 0.7766 (tppt) outliers start: 24 outliers final: 20 residues processed: 101 average time/residue: 0.0824 time to fit residues: 12.8551 Evaluate side-chains 99 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 91 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114551 restraints weight = 15763.286| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.97 r_work: 0.3428 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10646 Z= 0.142 Angle : 0.565 9.152 14896 Z= 0.314 Chirality : 0.037 0.245 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.704 168.160 2389 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.47 % Allowed : 20.82 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.28), residues: 956 helix: 1.64 (0.24), residues: 518 sheet: -0.41 (0.60), residues: 64 loop : -1.46 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 176 TYR 0.021 0.001 TYR E 241 PHE 0.015 0.001 PHE A 292 TRP 0.012 0.001 TRP A 41 HIS 0.002 0.000 HIS E 408 Details of bonding type rmsd covalent geometry : bond 0.00317 (10638) covalent geometry : angle 0.56429 (14892) hydrogen bonds : bond 0.03798 ( 520) hydrogen bonds : angle 3.90139 ( 1411) metal coordination : bond 0.00333 ( 8) metal coordination : angle 1.36724 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.41 seconds wall clock time: 36 minutes 38.30 seconds (2198.30 seconds total)