Starting phenix.real_space_refine on Mon Jul 28 06:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pr5_20457/07_2025/6pr5_20457.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pr5_20457/07_2025/6pr5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pr5_20457/07_2025/6pr5_20457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pr5_20457/07_2025/6pr5_20457.map" model { file = "/net/cci-nas-00/data/ceres_data/6pr5_20457/07_2025/6pr5_20457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pr5_20457/07_2025/6pr5_20457.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: 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ASP: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: 6.47, per 1000 atoms: 0.63 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: 2.51 Conformation dependent library (CDL) restraints added in 868.0 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: 3.92 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: 3.85 Time building geometry restraints manager: 2.96 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.360 Find NCS groups from input model: 0.240 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.017 0.002 TRP A 41 HIS 0.006 0.001 HIS A 483 PHE 0.015 0.002 PHE A 292 TYR 0.012 0.002 TYR E 394 ARG 0.007 0.001 ARG A 477 Details of bonding type rmsd hydrogen bonds : bond 0.11626 ( 520) hydrogen bonds : angle 6.07128 ( 1411) metal coordination : bond 0.19508 ( 8) metal coordination : angle 20.53761 ( 4) covalent geometry : bond 0.00802 (10638) covalent geometry : angle 0.77552 (14892) *********************** 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 : 0.977 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: 0.7805 (m90) cc_final: 0.7395 (m170) REVERT: E 173 MET cc_start: 0.7295 (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: 0.8102 (tt) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.2492 time to fit residues: 39.9614 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 : 0.963 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113741 restraints weight = 15890.402| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.95 r_work: 0.3404 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10646 Z= 0.150 Angle : 0.590 10.246 14896 Z= 0.328 Chirality : 0.038 0.178 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.901 160.012 2392 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 2.00 % Allowed : 13.18 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 956 helix: 0.12 (0.23), residues: 498 sheet: -0.98 (0.59), residues: 64 loop : -2.05 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 41 HIS 0.002 0.001 HIS A 408 PHE 0.012 0.002 PHE A 180 TYR 0.014 0.001 TYR E 241 ARG 0.002 0.000 ARG E 437 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 520) hydrogen bonds : angle 4.40055 ( 1411) metal coordination : bond 0.01355 ( 8) metal coordination : angle 2.47752 ( 4) covalent geometry : bond 0.00329 (10638) covalent geometry : angle 0.58838 (14892) *********************** 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 123 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 145 SER cc_start: 0.8887 (p) cc_final: 0.8637 (m) REVERT: A 219 MET cc_start: 0.8941 (ptm) cc_final: 0.8717 (ptm) REVERT: A 442 ARG cc_start: 0.8645 (mpt-90) cc_final: 0.8405 (mtt90) REVERT: A 470 ASP cc_start: 0.9025 (t70) cc_final: 0.8822 (t70) REVERT: E 173 MET cc_start: 0.8053 (mtp) cc_final: 0.7675 (mtp) REVERT: E 184 LYS cc_start: 0.8523 (tttt) cc_final: 0.7646 (tppt) REVERT: E 307 HIS cc_start: 0.8291 (m90) cc_final: 0.7948 (m-70) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.2312 time to fit residues: 38.8880 Evaluate side-chains 93 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 58 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.141432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115297 restraints weight = 16144.033| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.99 r_work: 0.3428 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2061 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= 0.139 Angle : 0.556 8.371 14896 Z= 0.312 Chirality : 0.037 0.183 1690 Planarity : 0.004 0.038 1452 Dihedral : 25.843 164.025 2389 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 1.76 % Allowed : 16.35 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.27), residues: 956 helix: 1.01 (0.24), residues: 502 sheet: -0.77 (0.58), residues: 64 loop : -1.83 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.002 0.001 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.010 0.001 TYR A 62 ARG 0.003 0.000 ARG E 437 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 520) hydrogen bonds : angle 4.04820 ( 1411) metal coordination : bond 0.00490 ( 8) metal coordination : angle 1.85699 ( 4) covalent geometry : bond 0.00305 (10638) covalent geometry : angle 0.55507 (14892) *********************** 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 113 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 145 SER cc_start: 0.8934 (p) cc_final: 0.8528 (m) REVERT: A 219 MET cc_start: 0.8974 (ptm) cc_final: 0.8722 (ptm) REVERT: A 315 ASP cc_start: 0.8263 (m-30) cc_final: 0.7963 (m-30) REVERT: E 173 MET cc_start: 0.8027 (mtp) cc_final: 0.7661 (mtp) REVERT: E 184 LYS cc_start: 0.8486 (tttt) cc_final: 0.7589 (tppt) REVERT: E 307 HIS cc_start: 0.8322 (m90) cc_final: 0.8084 (m90) REVERT: E 470 ASP cc_start: 0.8628 (t70) cc_final: 0.8350 (t0) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.2012 time to fit residues: 33.0613 Evaluate side-chains 91 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 395 VAL 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 65 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 141 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 = 0.3817 r_free = 0.3817 target = 0.136498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110685 restraints weight = 16206.315| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.93 r_work: 0.3356 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 10646 Z= 0.240 Angle : 0.629 10.489 14896 Z= 0.343 Chirality : 0.041 0.201 1690 Planarity : 0.004 0.040 1452 Dihedral : 26.060 165.214 2389 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 2.47 % Allowed : 17.65 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.27), residues: 956 helix: 1.00 (0.23), residues: 512 sheet: -0.77 (0.59), residues: 64 loop : -1.73 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.004 0.001 HIS A 483 PHE 0.012 0.002 PHE A 180 TYR 0.022 0.002 TYR E 73 ARG 0.005 0.001 ARG E 437 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 520) hydrogen bonds : angle 4.16421 ( 1411) metal coordination : bond 0.01185 ( 8) metal coordination : angle 2.38834 ( 4) covalent geometry : bond 0.00557 (10638) covalent geometry : angle 0.62792 (14892) *********************** 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 98 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.974 Fit side-chains REVERT: A 124 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8894 (p90) REVERT: A 219 MET cc_start: 0.9086 (ptm) cc_final: 0.8848 (ptm) REVERT: A 315 ASP cc_start: 0.8370 (m-30) cc_final: 0.8017 (m-30) REVERT: E 173 MET cc_start: 0.8136 (mtp) cc_final: 0.7768 (mtp) REVERT: E 184 LYS cc_start: 0.8536 (tttt) cc_final: 0.7702 (tppt) outliers start: 21 outliers final: 17 residues processed: 94 average time/residue: 0.1827 time to fit residues: 26.5086 Evaluate side-chains 90 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 198 ASP 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 221 THR Chi-restraints excluded: chain E residue 395 VAL 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 16 optimal weight: 0.0970 chunk 21 optimal weight: 0.4980 chunk 104 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 62 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.142193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116602 restraints weight = 15757.927| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.88 r_work: 0.3422 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10646 Z= 0.127 Angle : 0.530 6.389 14896 Z= 0.299 Chirality : 0.036 0.210 1690 Planarity : 0.003 0.039 1452 Dihedral : 25.740 164.742 2389 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 2.00 % Allowed : 19.41 % Favored : 78.59 % 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: 0.19 (0.27), residues: 956 helix: 1.40 (0.24), residues: 516 sheet: -0.56 (0.59), residues: 64 loop : -1.59 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.002 0.000 HIS E 408 PHE 0.013 0.001 PHE A 292 TYR 0.012 0.001 TYR E 73 ARG 0.002 0.000 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 520) hydrogen bonds : angle 3.88810 ( 1411) metal coordination : bond 0.00474 ( 8) metal coordination : angle 1.58914 ( 4) covalent geometry : bond 0.00276 (10638) covalent geometry : angle 0.52929 (14892) *********************** 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 112 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.915 Fit side-chains REVERT: A 145 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8484 (m) REVERT: E 173 MET cc_start: 0.8062 (mtp) cc_final: 0.7709 (mtp) REVERT: E 184 LYS cc_start: 0.8519 (tttt) cc_final: 0.7656 (tppt) REVERT: E 334 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8072 (p) REVERT: E 470 ASP cc_start: 0.8317 (t70) cc_final: 0.8018 (t0) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.2001 time to fit residues: 32.0268 Evaluate side-chains 94 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 145 SER 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 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 334 THR Chi-restraints excluded: chain E residue 395 VAL 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 97 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.139679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112880 restraints weight = 16256.962| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.02 r_work: 0.3391 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10646 Z= 0.175 Angle : 0.575 9.340 14896 Z= 0.317 Chirality : 0.038 0.206 1690 Planarity : 0.004 0.037 1452 Dihedral : 25.839 166.573 2389 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.47 % Allowed : 20.71 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.27), residues: 956 helix: 1.44 (0.24), residues: 516 sheet: -0.51 (0.60), residues: 64 loop : -1.55 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 PHE 0.012 0.001 PHE A 180 TYR 0.015 0.001 TYR E 241 ARG 0.005 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 520) hydrogen bonds : angle 3.95937 ( 1411) metal coordination : bond 0.00663 ( 8) metal coordination : angle 1.60252 ( 4) covalent geometry : bond 0.00399 (10638) covalent geometry : angle 0.57449 (14892) *********************** 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 104 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.048 Fit side-chains REVERT: A 124 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8697 (p90) REVERT: E 173 MET cc_start: 0.7859 (mtp) cc_final: 0.7507 (mtp) REVERT: E 184 LYS cc_start: 0.8435 (tttt) cc_final: 0.7582 (tppt) REVERT: E 334 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8191 (p) REVERT: E 470 ASP cc_start: 0.8202 (t70) cc_final: 0.7885 (t0) outliers start: 21 outliers final: 18 residues processed: 101 average time/residue: 0.1781 time to fit residues: 27.8198 Evaluate side-chains 98 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 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 149 THR 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 395 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 44 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.143282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117602 restraints weight = 16101.309| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.89 r_work: 0.3464 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10646 Z= 0.128 Angle : 0.534 9.212 14896 Z= 0.298 Chirality : 0.036 0.220 1690 Planarity : 0.003 0.038 1452 Dihedral : 25.637 166.126 2389 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.94 % Allowed : 20.59 % 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 (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: 0.49 (0.28), residues: 956 helix: 1.65 (0.24), residues: 516 sheet: -0.56 (0.59), residues: 64 loop : -1.45 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.003 0.000 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.014 0.001 TYR E 241 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 520) hydrogen bonds : angle 3.80512 ( 1411) metal coordination : bond 0.00314 ( 8) metal coordination : angle 1.36814 ( 4) covalent geometry : bond 0.00281 (10638) covalent geometry : angle 0.53361 (14892) *********************** 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 122 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.037 Fit side-chains REVERT: A 124 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8445 (p90) REVERT: A 145 SER cc_start: 0.8945 (p) cc_final: 0.8472 (m) REVERT: E 57 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6224 (pt0) REVERT: E 173 MET cc_start: 0.8034 (mtp) cc_final: 0.7660 (mtp) REVERT: E 184 LYS cc_start: 0.8517 (tttt) cc_final: 0.7683 (tppt) REVERT: E 280 MET cc_start: 0.8148 (ttt) cc_final: 0.7945 (ttp) REVERT: E 334 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8224 (p) REVERT: E 470 ASP cc_start: 0.8152 (t70) cc_final: 0.7922 (t0) outliers start: 25 outliers final: 19 residues processed: 117 average time/residue: 0.1757 time to fit residues: 31.6821 Evaluate side-chains 101 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 E residue 57 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 253 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 395 VAL 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 93 optimal weight: 0.0980 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.143960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117921 restraints weight = 16016.757| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.97 r_work: 0.3468 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10646 Z= 0.129 Angle : 0.545 9.077 14896 Z= 0.304 Chirality : 0.036 0.229 1690 Planarity : 0.003 0.037 1452 Dihedral : 25.577 168.310 2389 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.71 % Allowed : 21.06 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.28), residues: 956 helix: 1.75 (0.24), residues: 516 sheet: -0.37 (0.59), residues: 64 loop : -1.40 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.002 0.000 HIS E 408 PHE 0.010 0.001 PHE A 180 TYR 0.015 0.001 TYR E 241 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 520) hydrogen bonds : angle 3.75040 ( 1411) metal coordination : bond 0.00339 ( 8) metal coordination : angle 1.59289 ( 4) covalent geometry : bond 0.00286 (10638) covalent geometry : angle 0.54436 (14892) *********************** 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 107 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.834 Fit side-chains REVERT: A 124 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8455 (p90) REVERT: A 212 HIS cc_start: 0.8443 (m90) cc_final: 0.7996 (m170) REVERT: E 173 MET cc_start: 0.7777 (mtp) cc_final: 0.7450 (mtp) REVERT: E 184 LYS cc_start: 0.8554 (tttt) cc_final: 0.7699 (tppt) REVERT: E 280 MET cc_start: 0.8073 (ttt) cc_final: 0.7873 (ttp) REVERT: E 334 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8108 (p) REVERT: E 470 ASP cc_start: 0.8043 (t70) cc_final: 0.7804 (t0) outliers start: 23 outliers final: 19 residues processed: 103 average time/residue: 0.1805 time to fit residues: 28.2673 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 : 0.947 ------------------------------------------------------------------------------- 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 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 253 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 395 VAL 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 64 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107786 restraints weight = 16212.356| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.06 r_work: 0.3325 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10646 Z= 0.281 Angle : 0.679 10.118 14896 Z= 0.369 Chirality : 0.043 0.257 1690 Planarity : 0.005 0.050 1452 Dihedral : 26.125 167.191 2389 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.82 % Allowed : 21.53 % Favored : 75.65 % 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: 0.18 (0.27), residues: 956 helix: 1.25 (0.23), residues: 516 sheet: -0.51 (0.59), residues: 64 loop : -1.38 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 295 HIS 0.005 0.001 HIS E 408 PHE 0.012 0.002 PHE E 292 TYR 0.019 0.002 TYR E 241 ARG 0.006 0.001 ARG E 437 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 520) hydrogen bonds : angle 4.24774 ( 1411) metal coordination : bond 0.01161 ( 8) metal coordination : angle 2.48640 ( 4) covalent geometry : bond 0.00656 (10638) covalent geometry : angle 0.67820 (14892) *********************** 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 91 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.942 Fit side-chains REVERT: E 173 MET cc_start: 0.7825 (mtp) cc_final: 0.7489 (mtp) REVERT: E 184 LYS cc_start: 0.8476 (tttt) cc_final: 0.7718 (tppt) REVERT: E 233 GLU cc_start: 0.6948 (pp20) cc_final: 0.6740 (pp20) outliers start: 24 outliers final: 21 residues processed: 90 average time/residue: 0.2062 time to fit residues: 27.5208 Evaluate side-chains 83 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 150 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 198 ASP 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 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 395 VAL 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 19 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.0030 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115851 restraints weight = 15882.256| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.99 r_work: 0.3448 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10646 Z= 0.133 Angle : 0.560 7.498 14896 Z= 0.314 Chirality : 0.037 0.232 1690 Planarity : 0.003 0.039 1452 Dihedral : 25.702 167.096 2389 Min Nonbonded Distance : 1.405 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.24 % Allowed : 21.29 % 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 (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: 0.53 (0.28), residues: 956 helix: 1.63 (0.24), residues: 516 sheet: -0.47 (0.58), residues: 64 loop : -1.35 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 41 HIS 0.002 0.000 HIS E 408 PHE 0.014 0.001 PHE A 292 TYR 0.014 0.001 TYR E 241 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 520) hydrogen bonds : angle 3.91256 ( 1411) metal coordination : bond 0.00434 ( 8) metal coordination : angle 1.56044 ( 4) covalent geometry : bond 0.00291 (10638) covalent geometry : angle 0.55919 (14892) ********************** 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 100 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.213 Fit side-chains REVERT: A 124 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8005 (p90) REVERT: E 173 MET cc_start: 0.7757 (mtp) cc_final: 0.7408 (mtp) REVERT: E 184 LYS cc_start: 0.8497 (tttt) cc_final: 0.7675 (tppt) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.1959 time to fit residues: 29.0803 Evaluate side-chains 93 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 395 VAL 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 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115453 restraints weight = 15791.625| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.96 r_work: 0.3439 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2961 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= 0.141 Angle : 0.573 10.348 14896 Z= 0.317 Chirality : 0.037 0.251 1690 Planarity : 0.004 0.038 1452 Dihedral : 25.684 169.401 2389 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.24 % Allowed : 21.53 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.28), residues: 956 helix: 1.70 (0.24), residues: 516 sheet: -0.24 (0.58), residues: 64 loop : -1.31 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 41 HIS 0.003 0.000 HIS E 408 PHE 0.011 0.001 PHE A 180 TYR 0.015 0.001 TYR E 241 ARG 0.005 0.000 ARG E 176 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 520) hydrogen bonds : angle 3.87567 ( 1411) metal coordination : bond 0.00403 ( 8) metal coordination : angle 1.68859 ( 4) covalent geometry : bond 0.00316 (10638) covalent geometry : angle 0.57285 (14892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.56 seconds wall clock time: 84 minutes 30.43 seconds (5070.43 seconds total)