Starting phenix.real_space_refine on Fri Sep 11 12:54:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.map" model { file = "/net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xdg_22137/09_2026/6xdg_22137.cif" } resolution = 3.9 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1514 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5058 2.51 5 N 1320 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8004 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1572 Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain: "B" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1603 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Chain breaks: 1 Chain: "C" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1604 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1565 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 MAN F 4 " occ=0.70 ... (9 atoms not shown) pdb=" O6 MAN F 4 " occ=0.70 Time building chain proxies: 1.72, per 1000 atoms: 0.21 Number of scatterers: 8004 At special positions: 0 Unit cell: (72.25, 119.85, 150.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1594 8.00 N 1320 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 197 " distance=2.03 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 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG F 1 " - " ASN E 343 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 385.3 milliseconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 8.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 389 removed outlier: 3.753A pdb=" N ASP E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.489A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 189 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.257A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.728A pdb=" N SER B 195 " --> pdb=" O PRO B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.823A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.975A pdb=" N LEU C 196 " --> pdb=" O SER C 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.798A pdb=" N GLN A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.996A pdb=" N HIS A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.820A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.758A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.431A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D 89 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.513A pdb=" N SER D 114 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 162 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 153 through 155 removed outlier: 3.730A pdb=" N GLN D 155 " --> pdb=" O TRP D 148 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.755A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 71 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.739A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 99 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.658A pdb=" N THR B 114 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.738A pdb=" N SER B 127 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 143 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 187 " --> pdb=" O CYS B 147 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 149 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 185 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER B 184 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA B 175 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 186 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.717A pdb=" N THR B 158 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.922A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.578A pdb=" N TYR C 59 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 50 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 131 removed outlier: 4.472A pdb=" N SER C 127 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 150 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 145 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 187 " --> pdb=" O CYS C 147 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 205 through 206 removed outlier: 3.515A pdb=" N VAL C 205 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 214 " --> pdb=" O VAL C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.737A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.444A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 40 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 87 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 92 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 100 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 118 through 122 removed outlier: 3.573A pdb=" N PHE A 122 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 137 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER A 141 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 178 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 169 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 118 through 122 removed outlier: 3.573A pdb=" N PHE A 122 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 137 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.565A pdb=" N TRP A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 198 " --> pdb=" O ALA A 151 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2535 1.35 - 1.47: 2165 1.47 - 1.59: 3460 1.59 - 1.71: 0 1.71 - 1.83: 39 Bond restraints: 8199 Sorted by residual: bond pdb=" C PHE E 497 " pdb=" N GLN E 498 " ideal model delta sigma weight residual 1.329 1.293 0.035 1.60e-02 3.91e+03 4.86e+00 bond pdb=" N VAL B 176 " pdb=" CA VAL B 176 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.25e-02 6.40e+03 2.15e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.444 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CA VAL D 110 " pdb=" CB VAL D 110 " ideal model delta sigma weight residual 1.553 1.544 0.009 7.40e-03 1.83e+04 1.44e+00 ... (remaining 8194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10805 1.62 - 3.24: 296 3.24 - 4.86: 49 4.86 - 6.49: 13 6.49 - 8.11: 8 Bond angle restraints: 11171 Sorted by residual: angle pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta sigma weight residual 120.49 113.22 7.27 1.42e+00 4.96e-01 2.62e+01 angle pdb=" C TYR A 51 " pdb=" N ASP A 52 " pdb=" CA ASP A 52 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C VAL A 53 " pdb=" N SER A 54 " pdb=" CA SER A 54 " ideal model delta sigma weight residual 120.23 127.04 -6.81 1.67e+00 3.59e-01 1.66e+01 angle pdb=" N SER C 100 " pdb=" CA SER C 100 " pdb=" C SER C 100 " ideal model delta sigma weight residual 110.33 114.61 -4.28 1.29e+00 6.01e-01 1.10e+01 angle pdb=" N ASP A 52 " pdb=" CA ASP A 52 " pdb=" C ASP A 52 " ideal model delta sigma weight residual 110.80 117.69 -6.89 2.13e+00 2.20e-01 1.05e+01 ... (remaining 11166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4397 17.29 - 34.59: 365 34.59 - 51.88: 61 51.88 - 69.17: 9 69.17 - 86.47: 6 Dihedral angle restraints: 4838 sinusoidal: 1818 harmonic: 3020 Sorted by residual: dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP A 52 " pdb=" C ASP A 52 " pdb=" N VAL A 53 " pdb=" CA VAL A 53 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASP B 108 " pdb=" C ASP B 108 " pdb=" N TYR B 109 " pdb=" CA TYR B 109 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 4835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1150 0.081 - 0.162: 109 0.162 - 0.244: 0 0.244 - 0.325: 2 0.325 - 0.406: 1 Chirality restraints: 1262 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.12e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.62e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.76e+01 ... (remaining 1259 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 155 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO C 156 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 110 " -0.016 2.00e-02 2.50e+03 9.78e-03 2.39e+00 pdb=" CG TRP B 110 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP B 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 110 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 110 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO E 463 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " 0.020 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 317 2.68 - 3.24: 8293 3.24 - 3.79: 12628 3.79 - 4.35: 16251 4.35 - 4.90: 25992 Nonbonded interactions: 63481 Sorted by model distance: nonbonded pdb=" OG SER D 121 " pdb=" O PRO B 130 " model vdw 2.127 3.040 nonbonded pdb=" O PRO C 130 " pdb=" OG SER A 125 " model vdw 2.135 3.040 nonbonded pdb=" O TYR D 186 " pdb=" OH TYR D 192 " model vdw 2.140 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 22 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP A 142 " pdb=" NE2 GLN A 171 " model vdw 2.171 3.120 ... (remaining 63476 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 'B' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ id 79 through 87 or resid 89 through 97 or resid 109 through 220)) selection = (chain 'C' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ id 79 through 87 or resid 89 through 97 or resid 109 through 220)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 8.930 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.004 0.065 8213 Z= 0.210 Angle : 0.897 46.634 11203 Z= 0.419 Chirality : 0.046 0.406 1262 Planarity : 0.004 0.042 1425 Dihedral : 12.946 86.466 2888 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.82 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -3.87 (0.23), residues: 1030 helix: -3.19 (0.52), residues: 48 sheet: -2.30 (0.24), residues: 377 loop : -2.77 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.014 0.001 TYR E 495 PHE 0.013 0.002 PHE C 68 TRP 0.025 0.002 TRP B 110 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 ( 8199) covalent geometry : angle 0.70083 / 0.37 (11171) SS BOND : bond 0.00292 / 0.17 ( 10) SS BOND : angle 1.07632 / 0.64 ( 20) hydrogen bonds : bond 0.33702 / 21.42 ( 205) hydrogen bonds : angle 11.45147 / 7.95 ( 531) link_ALPHA1-6 : bond 0.06424 / 3.38 ( 1) link_ALPHA1-6 : angle 12.26008 / 6.52 ( 3) link_BETA1-4 : bond 0.06496 / 3.26 ( 2) link_BETA1-4 : angle 22.48496 / 14.03 ( 6) link_NAG-ASN : bond 0.00253 / 0.13 ( 1) link_NAG-ASN : angle 2.27813 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9165 (pp20) cc_final: 0.8961 (pp20) REVERT: E 386 LYS cc_start: 0.9132 (mptt) cc_final: 0.8812 (tptt) REVERT: E 406 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8665 (mp0) REVERT: E 432 CYS cc_start: 0.7903 (t) cc_final: 0.7527 (m) REVERT: E 465 GLU cc_start: 0.7124 (tt0) cc_final: 0.6806 (tt0) REVERT: E 471 GLU cc_start: 0.8883 (tp30) cc_final: 0.8616 (tm-30) REVERT: D 93 ASN cc_start: 0.8525 (m110) cc_final: 0.8140 (t0) REVERT: D 105 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8111 (pt0) REVERT: D 142 ARG cc_start: 0.8989 (tmt170) cc_final: 0.8743 (ttp80) REVERT: D 187 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8841 (mm-30) REVERT: B 199 GLN cc_start: 0.8327 (mt0) cc_final: 0.8068 (tp40) REVERT: B 216 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8728 (ttpp) REVERT: C 4 LEU cc_start: 0.8118 (mt) cc_final: 0.7853 (mt) REVERT: A 49 MET cc_start: 0.8318 (mmm) cc_final: 0.7818 (mmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1148 time to fit residues: 19.2935 Evaluate side-chains 87 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 388 ASN E 474 GLN E 487 ASN D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS D 210 ASN B 82 GLN B 178 GLN B 207 HIS C 1 GLN C 162 ASN C 199 GLN C 204 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.080690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.053956 restraints weight = 46062.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.056735 restraints weight = 19194.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058497 restraints weight = 11378.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059582 restraints weight = 8122.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060221 restraints weight = 6543.545| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8213 Z= 0.211 Angle : 0.752 10.934 11203 Z= 0.385 Chirality : 0.046 0.181 1262 Planarity : 0.005 0.072 1425 Dihedral : 5.427 30.189 1130 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.84 % Favored : 90.86 % Rotamer: Outliers : 1.35 % Allowed : 13.13 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.14 (0.24), residues: 1030 helix: -2.52 (0.51), residues: 60 sheet: -1.59 (0.26), residues: 373 loop : -2.43 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 98 TYR 0.017 0.002 TYR C 102 PHE 0.021 0.002 PHE E 400 TRP 0.018 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 8199) covalent geometry : angle 0.74160 / 0.38 (11171) SS BOND : bond 0.00646 / 0.47 ( 10) SS BOND : angle 1.94828 / 1.10 ( 20) hydrogen bonds : bond 0.05919 / 3.82 ( 205) hydrogen bonds : angle 8.37883 / 5.85 ( 531) link_ALPHA1-6 : bond 0.01058 / 0.56 ( 1) link_ALPHA1-6 : angle 1.63484 / 0.93 ( 3) link_BETA1-4 : bond 0.00916 / 0.44 ( 2) link_BETA1-4 : angle 4.11237 / 2.27 ( 6) link_NAG-ASN : bond 0.00294 / 0.15 ( 1) link_NAG-ASN : angle 1.75452 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9151 (mptt) cc_final: 0.8808 (tptt) REVERT: E 406 GLU cc_start: 0.9403 (mt-10) cc_final: 0.8589 (mp0) REVERT: E 465 GLU cc_start: 0.7391 (tt0) cc_final: 0.7052 (tt0) REVERT: D 93 ASN cc_start: 0.8800 (m-40) cc_final: 0.8335 (t0) REVERT: D 105 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8155 (pt0) REVERT: D 142 ARG cc_start: 0.8907 (tmt170) cc_final: 0.8519 (ttp80) REVERT: D 187 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8708 (mm-30) REVERT: B 32 TYR cc_start: 0.8452 (m-80) cc_final: 0.7852 (m-10) REVERT: B 199 GLN cc_start: 0.8442 (mt0) cc_final: 0.8134 (tp40) REVERT: B 216 LYS cc_start: 0.9239 (ttmm) cc_final: 0.8778 (ttpp) REVERT: B 217 LYS cc_start: 0.8798 (tppp) cc_final: 0.8573 (tptp) REVERT: C 4 LEU cc_start: 0.8441 (mt) cc_final: 0.8232 (mt) REVERT: A 49 MET cc_start: 0.8431 (mmm) cc_final: 0.7878 (mmm) outliers start: 11 outliers final: 5 residues processed: 116 average time/residue: 0.1082 time to fit residues: 16.2055 Evaluate side-chains 92 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain A residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 50.0000 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** 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 = 0.3749 r_free = 0.3749 target = 0.079699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051982 restraints weight = 66479.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055147 restraints weight = 23205.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.057122 restraints weight = 12732.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058318 restraints weight = 8653.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059047 restraints weight = 6763.491| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8213 Z= 0.234 Angle : 0.729 10.392 11203 Z= 0.374 Chirality : 0.045 0.161 1262 Planarity : 0.005 0.046 1425 Dihedral : 5.484 32.319 1130 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.84 % Favored : 90.86 % Rotamer: Outliers : 2.92 % Allowed : 14.03 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.25), residues: 1030 helix: -2.31 (0.54), residues: 61 sheet: -1.19 (0.27), residues: 375 loop : -2.23 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 98 TYR 0.016 0.002 TYR E 495 PHE 0.016 0.002 PHE E 400 TRP 0.019 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 ( 8199) covalent geometry : angle 0.72054 / 0.37 (11171) SS BOND : bond 0.00440 / 0.24 ( 10) SS BOND : angle 1.69580 / 1.05 ( 20) hydrogen bonds : bond 0.04681 / 3.03 ( 205) hydrogen bonds : angle 7.78398 / 5.42 ( 531) link_ALPHA1-6 : bond 0.01049 / 0.55 ( 1) link_ALPHA1-6 : angle 1.91023 / 1.03 ( 3) link_BETA1-4 : bond 0.00837 / 0.40 ( 2) link_BETA1-4 : angle 3.42843 / 1.84 ( 6) link_NAG-ASN : bond 0.00160 / 0.08 ( 1) link_NAG-ASN : angle 1.57642 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9128 (mptt) cc_final: 0.8796 (tptt) REVERT: E 406 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8652 (mp0) REVERT: E 424 LYS cc_start: 0.8969 (tptm) cc_final: 0.8714 (mptm) REVERT: E 465 GLU cc_start: 0.7357 (tt0) cc_final: 0.7040 (tt0) REVERT: D 93 ASN cc_start: 0.8855 (m-40) cc_final: 0.8378 (t0) REVERT: D 105 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8115 (pt0) REVERT: D 142 ARG cc_start: 0.8932 (tmt170) cc_final: 0.8500 (ttp80) REVERT: D 187 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8723 (mm-30) REVERT: B 199 GLN cc_start: 0.8458 (mt0) cc_final: 0.8117 (tp40) REVERT: B 216 LYS cc_start: 0.9271 (ttmm) cc_final: 0.8933 (ttpp) REVERT: C 147 CYS cc_start: 0.7716 (p) cc_final: 0.6491 (m) REVERT: A 38 TYR cc_start: 0.8172 (m-80) cc_final: 0.7860 (m-10) REVERT: A 49 MET cc_start: 0.8388 (mmm) cc_final: 0.7900 (mmm) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.1101 time to fit residues: 16.6803 Evaluate side-chains 100 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS B 82 GLN ** C 207 HIS ** 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 = 0.3745 r_free = 0.3745 target = 0.079674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052940 restraints weight = 45353.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055634 restraints weight = 19119.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.057322 restraints weight = 11378.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058357 restraints weight = 8174.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058989 restraints weight = 6632.784| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8213 Z= 0.232 Angle : 0.721 10.105 11203 Z= 0.373 Chirality : 0.045 0.203 1262 Planarity : 0.005 0.073 1425 Dihedral : 5.577 31.284 1130 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.23 % Favored : 90.48 % Rotamer: Outliers : 2.58 % Allowed : 16.61 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.25), residues: 1030 helix: -2.12 (0.52), residues: 67 sheet: -1.05 (0.26), residues: 393 loop : -2.17 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 98 TYR 0.016 0.002 TYR E 495 PHE 0.018 0.002 PHE E 400 TRP 0.015 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 ( 8199) covalent geometry : angle 0.71281 / 0.37 (11171) SS BOND : bond 0.00446 / 0.23 ( 10) SS BOND : angle 1.83594 / 1.02 ( 20) hydrogen bonds : bond 0.04128 / 2.68 ( 205) hydrogen bonds : angle 7.49835 / 5.22 ( 531) link_ALPHA1-6 : bond 0.01002 / 0.53 ( 1) link_ALPHA1-6 : angle 1.73642 / 0.95 ( 3) link_BETA1-4 : bond 0.00694 / 0.33 ( 2) link_BETA1-4 : angle 3.41771 / 1.83 ( 6) link_NAG-ASN : bond 0.00207 / 0.11 ( 1) link_NAG-ASN : angle 1.49833 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9113 (mptt) cc_final: 0.8787 (tptt) REVERT: E 406 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8669 (mp0) REVERT: E 424 LYS cc_start: 0.8970 (tptm) cc_final: 0.8720 (mptm) REVERT: E 465 GLU cc_start: 0.7439 (tt0) cc_final: 0.7093 (tt0) REVERT: E 471 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8414 (tm-30) REVERT: D 93 ASN cc_start: 0.8860 (m-40) cc_final: 0.8351 (t0) REVERT: D 105 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8132 (pt0) REVERT: D 142 ARG cc_start: 0.8874 (tmt170) cc_final: 0.8350 (ttp80) REVERT: B 76 LYS cc_start: 0.9599 (mtmm) cc_final: 0.9374 (mtmm) REVERT: B 199 GLN cc_start: 0.8570 (mt0) cc_final: 0.8269 (tp40) REVERT: B 216 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8281 (ttpp) REVERT: C 147 CYS cc_start: 0.7778 (p) cc_final: 0.6676 (m) REVERT: A 38 TYR cc_start: 0.8180 (m-80) cc_final: 0.7861 (m-10) REVERT: A 49 MET cc_start: 0.8411 (mmm) cc_final: 0.7914 (mmm) outliers start: 22 outliers final: 17 residues processed: 107 average time/residue: 0.1141 time to fit residues: 15.5996 Evaluate side-chains 101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 93 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 481 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.081217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054088 restraints weight = 51095.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057050 restraints weight = 19749.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058884 restraints weight = 11287.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.059966 restraints weight = 7892.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060542 restraints weight = 6328.188| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8213 Z= 0.157 Angle : 0.671 9.199 11203 Z= 0.346 Chirality : 0.045 0.192 1262 Planarity : 0.005 0.052 1425 Dihedral : 5.396 30.573 1130 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.55 % Favored : 91.25 % Rotamer: Outliers : 3.59 % Allowed : 16.27 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.26), residues: 1030 helix: -2.00 (0.56), residues: 61 sheet: -0.89 (0.27), residues: 380 loop : -1.94 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.011 0.001 TYR E 495 PHE 0.016 0.001 PHE E 400 TRP 0.011 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 8199) covalent geometry : angle 0.66481 / 0.34 (11171) SS BOND : bond 0.00343 / 0.17 ( 10) SS BOND : angle 1.46955 / 0.80 ( 20) hydrogen bonds : bond 0.03472 / 2.27 ( 205) hydrogen bonds : angle 7.12488 / 4.96 ( 531) link_ALPHA1-6 : bond 0.00999 / 0.53 ( 1) link_ALPHA1-6 : angle 1.65484 / 0.91 ( 3) link_BETA1-4 : bond 0.00636 / 0.30 ( 2) link_BETA1-4 : angle 3.11506 / 1.65 ( 6) link_NAG-ASN : bond 0.00050 / 0.03 ( 1) link_NAG-ASN : angle 1.15164 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9100 (mptt) cc_final: 0.8791 (tptt) REVERT: E 406 GLU cc_start: 0.9395 (mt-10) cc_final: 0.8650 (mp0) REVERT: E 465 GLU cc_start: 0.7355 (tt0) cc_final: 0.6982 (tt0) REVERT: D 93 ASN cc_start: 0.8827 (m-40) cc_final: 0.8375 (t0) REVERT: D 105 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8127 (pt0) REVERT: D 142 ARG cc_start: 0.8806 (tmt170) cc_final: 0.8340 (ttp80) REVERT: B 34 MET cc_start: 0.8254 (mmm) cc_final: 0.7963 (mmm) REVERT: B 199 GLN cc_start: 0.8528 (mt0) cc_final: 0.8260 (tp40) REVERT: B 213 LYS cc_start: 0.9355 (mtpt) cc_final: 0.8892 (tptt) REVERT: B 216 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8251 (ttpp) REVERT: C 147 CYS cc_start: 0.7786 (p) cc_final: 0.6720 (m) REVERT: A 38 TYR cc_start: 0.8150 (m-80) cc_final: 0.7882 (m-80) REVERT: A 49 MET cc_start: 0.8411 (mmm) cc_final: 0.7881 (mmm) outliers start: 31 outliers final: 23 residues processed: 121 average time/residue: 0.1047 time to fit residues: 16.6621 Evaluate side-chains 104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 165 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 8 optimal weight: 0.0980 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 76 optimal weight: 50.0000 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 354 ASN E 360 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN B 82 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.078879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051135 restraints weight = 59437.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.054247 restraints weight = 21867.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056156 restraints weight = 12093.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057333 restraints weight = 8283.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058037 restraints weight = 6510.489| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8213 Z= 0.219 Angle : 0.713 9.920 11203 Z= 0.365 Chirality : 0.045 0.189 1262 Planarity : 0.005 0.075 1425 Dihedral : 5.495 25.553 1130 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.23 % Favored : 90.48 % Rotamer: Outliers : 3.48 % Allowed : 18.18 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.26), residues: 1030 helix: -1.88 (0.57), residues: 61 sheet: -0.87 (0.28), residues: 371 loop : -1.88 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 98 TYR 0.029 0.002 TYR E 495 PHE 0.022 0.002 PHE E 497 TRP 0.015 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 ( 8199) covalent geometry : angle 0.70583 / 0.36 (11171) SS BOND : bond 0.00366 / 0.19 ( 10) SS BOND : angle 1.62505 / 0.83 ( 20) hydrogen bonds : bond 0.03721 / 2.44 ( 205) hydrogen bonds : angle 7.09543 / 4.95 ( 531) link_ALPHA1-6 : bond 0.00906 / 0.48 ( 1) link_ALPHA1-6 : angle 1.52720 / 0.84 ( 3) link_BETA1-4 : bond 0.00680 / 0.32 ( 2) link_BETA1-4 : angle 3.19107 / 1.66 ( 6) link_NAG-ASN : bond 0.00309 / 0.16 ( 1) link_NAG-ASN : angle 1.52048 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9108 (mptt) cc_final: 0.8792 (tptt) REVERT: E 406 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8674 (mp0) REVERT: E 465 GLU cc_start: 0.7429 (tt0) cc_final: 0.6660 (tt0) REVERT: D 93 ASN cc_start: 0.8882 (m-40) cc_final: 0.8443 (t0) REVERT: D 105 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8143 (pt0) REVERT: D 142 ARG cc_start: 0.8764 (tmt170) cc_final: 0.8284 (ttp80) REVERT: B 62 ASP cc_start: 0.8490 (t0) cc_final: 0.8201 (t0) REVERT: B 76 LYS cc_start: 0.9637 (mtmm) cc_final: 0.9399 (mtmm) REVERT: B 199 GLN cc_start: 0.8526 (mt0) cc_final: 0.8218 (tp40) REVERT: B 213 LYS cc_start: 0.9366 (mtpt) cc_final: 0.8899 (tptt) REVERT: B 216 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8305 (ttpp) REVERT: C 129 PHE cc_start: 0.8267 (m-10) cc_final: 0.8037 (m-10) REVERT: C 147 CYS cc_start: 0.7828 (p) cc_final: 0.6989 (m) REVERT: A 38 TYR cc_start: 0.8216 (m-80) cc_final: 0.7930 (m-80) REVERT: A 49 MET cc_start: 0.8414 (mmm) cc_final: 0.7883 (mmm) outliers start: 30 outliers final: 24 residues processed: 109 average time/residue: 0.1066 time to fit residues: 15.1201 Evaluate side-chains 103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 140 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 77 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 96 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.078777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.051110 restraints weight = 61565.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054287 restraints weight = 22382.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056211 restraints weight = 12325.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057389 restraints weight = 8427.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058106 restraints weight = 6607.033| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8213 Z= 0.220 Angle : 0.708 10.719 11203 Z= 0.364 Chirality : 0.045 0.185 1262 Planarity : 0.005 0.054 1425 Dihedral : 5.498 25.547 1130 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.94 % Favored : 90.77 % Rotamer: Outliers : 3.25 % Allowed : 18.18 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.26), residues: 1030 helix: -1.97 (0.56), residues: 64 sheet: -0.92 (0.27), residues: 383 loop : -1.79 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.038 0.002 TYR E 495 PHE 0.049 0.002 PHE E 497 TRP 0.017 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 ( 8199) covalent geometry : angle 0.70187 / 0.36 (11171) SS BOND : bond 0.00376 / 0.18 ( 10) SS BOND : angle 1.59917 / 0.84 ( 20) hydrogen bonds : bond 0.03640 / 2.38 ( 205) hydrogen bonds : angle 6.99859 / 4.88 ( 531) link_ALPHA1-6 : bond 0.00869 / 0.46 ( 1) link_ALPHA1-6 : angle 1.46146 / 0.80 ( 3) link_BETA1-4 : bond 0.00604 / 0.29 ( 2) link_BETA1-4 : angle 2.99672 / 1.55 ( 6) link_NAG-ASN : bond 0.00249 / 0.13 ( 1) link_NAG-ASN : angle 1.52138 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9108 (mptt) cc_final: 0.8805 (tptt) REVERT: E 406 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8683 (mp0) REVERT: D 93 ASN cc_start: 0.8898 (m-40) cc_final: 0.8478 (t0) REVERT: D 105 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8121 (pt0) REVERT: D 142 ARG cc_start: 0.8756 (tmt170) cc_final: 0.8259 (ttp80) REVERT: B 34 MET cc_start: 0.8285 (mmm) cc_final: 0.8063 (mmm) REVERT: B 62 ASP cc_start: 0.8515 (t0) cc_final: 0.8224 (t0) REVERT: B 199 GLN cc_start: 0.8508 (mt0) cc_final: 0.8167 (tp40) REVERT: B 213 LYS cc_start: 0.9361 (mtpt) cc_final: 0.8888 (tptt) REVERT: B 216 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8302 (ttpp) REVERT: C 129 PHE cc_start: 0.8257 (m-10) cc_final: 0.8005 (m-10) REVERT: C 147 CYS cc_start: 0.7782 (p) cc_final: 0.7018 (m) REVERT: A 38 TYR cc_start: 0.8244 (m-80) cc_final: 0.7970 (m-80) REVERT: A 49 MET cc_start: 0.8400 (mmm) cc_final: 0.7859 (mmm) outliers start: 28 outliers final: 26 residues processed: 104 average time/residue: 0.1107 time to fit residues: 15.3041 Evaluate side-chains 106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 140 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 0.0010 chunk 73 optimal weight: 9.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.081734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054958 restraints weight = 43772.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.057883 restraints weight = 17804.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.059654 restraints weight = 10282.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.060760 restraints weight = 7250.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061429 restraints weight = 5797.516| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8213 Z= 0.121 Angle : 0.685 10.688 11203 Z= 0.346 Chirality : 0.045 0.199 1262 Planarity : 0.005 0.076 1425 Dihedral : 5.202 27.857 1130 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.07 % Favored : 91.74 % Rotamer: Outliers : 2.69 % Allowed : 19.30 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -1.97 (0.27), residues: 1030 helix: -1.85 (0.57), residues: 64 sheet: -0.79 (0.28), residues: 379 loop : -1.60 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 408 TYR 0.025 0.001 TYR E 495 PHE 0.029 0.002 PHE E 497 TRP 0.014 0.002 TRP B 161 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8199) covalent geometry : angle 0.68070 / 0.34 (11171) SS BOND : bond 0.00404 / 0.19 ( 10) SS BOND : angle 1.33791 / 0.73 ( 20) hydrogen bonds : bond 0.02967 / 1.97 ( 205) hydrogen bonds : angle 6.65061 / 4.65 ( 531) link_ALPHA1-6 : bond 0.00825 / 0.43 ( 1) link_ALPHA1-6 : angle 1.40667 / 0.77 ( 3) link_BETA1-4 : bond 0.00559 / 0.27 ( 2) link_BETA1-4 : angle 2.50802 / 1.31 ( 6) link_NAG-ASN : bond 0.00183 / 0.10 ( 1) link_NAG-ASN : angle 0.99223 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9074 (mptt) cc_final: 0.8783 (tptt) REVERT: E 406 GLU cc_start: 0.9380 (mt-10) cc_final: 0.8666 (mp0) REVERT: E 465 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7369 (tt0) REVERT: E 468 ILE cc_start: 0.9288 (pt) cc_final: 0.8978 (tp) REVERT: D 93 ASN cc_start: 0.8740 (m-40) cc_final: 0.8331 (t0) REVERT: D 142 ARG cc_start: 0.8677 (tmt170) cc_final: 0.8168 (ttp80) REVERT: D 187 GLU cc_start: 0.9574 (tp30) cc_final: 0.9292 (pt0) REVERT: B 62 ASP cc_start: 0.8489 (t0) cc_final: 0.8179 (t0) REVERT: B 199 GLN cc_start: 0.8472 (mt0) cc_final: 0.8117 (tm-30) REVERT: B 216 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8131 (ttpp) REVERT: C 87 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8141 (mtm180) REVERT: C 129 PHE cc_start: 0.8219 (m-10) cc_final: 0.7935 (m-10) REVERT: C 147 CYS cc_start: 0.7705 (p) cc_final: 0.6904 (m) REVERT: A 38 TYR cc_start: 0.8041 (m-80) cc_final: 0.7822 (m-80) REVERT: A 49 MET cc_start: 0.8360 (mmm) cc_final: 0.7819 (mmm) outliers start: 23 outliers final: 20 residues processed: 113 average time/residue: 0.1080 time to fit residues: 16.2859 Evaluate side-chains 105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 56 optimal weight: 0.0020 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.078925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051991 restraints weight = 51668.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054839 restraints weight = 20129.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056623 restraints weight = 11481.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057710 restraints weight = 8016.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058269 restraints weight = 6398.633| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8213 Z= 0.225 Angle : 0.723 10.338 11203 Z= 0.371 Chirality : 0.045 0.179 1262 Planarity : 0.005 0.052 1425 Dihedral : 5.431 31.355 1130 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.91 % Favored : 89.89 % Rotamer: Outliers : 2.81 % Allowed : 20.20 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.27), residues: 1030 helix: -1.68 (0.58), residues: 63 sheet: -0.93 (0.27), residues: 394 loop : -1.64 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 408 TYR 0.038 0.002 TYR E 495 PHE 0.039 0.002 PHE E 497 TRP 0.030 0.002 TRP C 36 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 8199) covalent geometry : angle 0.71784 / 0.37 (11171) SS BOND : bond 0.00375 / 0.19 ( 10) SS BOND : angle 1.35412 / 0.72 ( 20) hydrogen bonds : bond 0.03405 / 2.24 ( 205) hydrogen bonds : angle 6.74052 / 4.71 ( 531) link_ALPHA1-6 : bond 0.00854 / 0.45 ( 1) link_ALPHA1-6 : angle 1.43981 / 0.79 ( 3) link_BETA1-4 : bond 0.00503 / 0.24 ( 2) link_BETA1-4 : angle 2.72430 / 1.39 ( 6) link_NAG-ASN : bond 0.00343 / 0.18 ( 1) link_NAG-ASN : angle 1.67543 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9095 (mptt) cc_final: 0.8817 (tptt) REVERT: E 406 GLU cc_start: 0.9420 (mt-10) cc_final: 0.8704 (mp0) REVERT: E 468 ILE cc_start: 0.9306 (pt) cc_final: 0.9008 (tp) REVERT: D 93 ASN cc_start: 0.8850 (m-40) cc_final: 0.8448 (t0) REVERT: D 105 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7767 (mp0) REVERT: D 142 ARG cc_start: 0.8738 (tmt170) cc_final: 0.8191 (ttp80) REVERT: B 62 ASP cc_start: 0.8517 (t0) cc_final: 0.8235 (t0) REVERT: B 199 GLN cc_start: 0.8433 (mt0) cc_final: 0.8113 (tp40) REVERT: B 216 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8278 (ttpp) REVERT: C 129 PHE cc_start: 0.8239 (m-10) cc_final: 0.7970 (m-10) REVERT: C 147 CYS cc_start: 0.7766 (p) cc_final: 0.7032 (m) REVERT: A 38 TYR cc_start: 0.8213 (m-80) cc_final: 0.7971 (m-80) REVERT: A 49 MET cc_start: 0.8383 (mmm) cc_final: 0.7850 (mmm) outliers start: 24 outliers final: 19 residues processed: 104 average time/residue: 0.1107 time to fit residues: 15.2880 Evaluate side-chains 102 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 101 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 23 optimal weight: 0.2980 chunk 25 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.081038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052762 restraints weight = 78749.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056356 restraints weight = 24632.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058510 restraints weight = 12823.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059845 restraints weight = 8434.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060629 restraints weight = 6449.848| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8213 Z= 0.147 Angle : 0.709 10.517 11203 Z= 0.359 Chirality : 0.045 0.185 1262 Planarity : 0.005 0.079 1425 Dihedral : 5.307 31.263 1130 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.07 % Favored : 91.64 % Rotamer: Outliers : 2.36 % Allowed : 20.88 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.90 (0.27), residues: 1030 helix: -1.73 (0.58), residues: 63 sheet: -0.80 (0.28), residues: 380 loop : -1.52 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.031 0.002 TYR A 176 PHE 0.026 0.002 PHE E 497 TRP 0.026 0.002 TRP C 36 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8199) covalent geometry : angle 0.70569 / 0.36 (11171) SS BOND : bond 0.00392 / 0.19 ( 10) SS BOND : angle 1.25645 / 0.68 ( 20) hydrogen bonds : bond 0.03160 / 2.07 ( 205) hydrogen bonds : angle 6.57885 / 4.63 ( 531) link_ALPHA1-6 : bond 0.00668 / 0.35 ( 1) link_ALPHA1-6 : angle 1.26975 / 0.70 ( 3) link_BETA1-4 : bond 0.00560 / 0.27 ( 2) link_BETA1-4 : angle 2.31847 / 1.19 ( 6) link_NAG-ASN : bond 0.00009 / 0.00 ( 1) link_NAG-ASN : angle 1.26372 / 0.73 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9076 (mptt) cc_final: 0.8811 (tptt) REVERT: E 406 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8691 (mp0) REVERT: E 468 ILE cc_start: 0.9306 (pt) cc_final: 0.9022 (tp) REVERT: E 513 LEU cc_start: 0.9369 (mp) cc_final: 0.9042 (tp) REVERT: D 93 ASN cc_start: 0.8794 (m-40) cc_final: 0.8411 (t0) REVERT: D 142 ARG cc_start: 0.8669 (tmt170) cc_final: 0.8126 (ttp80) REVERT: B 62 ASP cc_start: 0.8514 (t0) cc_final: 0.8225 (t0) REVERT: B 199 GLN cc_start: 0.8428 (mt0) cc_final: 0.8062 (tm-30) REVERT: B 216 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8181 (ttpp) REVERT: C 129 PHE cc_start: 0.8168 (m-10) cc_final: 0.7875 (m-10) REVERT: C 147 CYS cc_start: 0.7658 (p) cc_final: 0.6882 (m) REVERT: A 49 MET cc_start: 0.8395 (mmm) cc_final: 0.7837 (mmm) outliers start: 20 outliers final: 18 residues processed: 107 average time/residue: 0.1075 time to fit residues: 15.1619 Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 101 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 40 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 33 optimal weight: 10.0000 chunk 80 optimal weight: 0.0470 chunk 84 optimal weight: 2.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN ** C 207 HIS ** 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 = 0.3765 r_free = 0.3765 target = 0.082253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054532 restraints weight = 66383.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.057911 restraints weight = 22634.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060003 restraints weight = 12091.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.061254 restraints weight = 8084.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 75)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.062094 restraints weight = 6260.088| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8213 Z= 0.128 Angle : 0.706 12.057 11203 Z= 0.355 Chirality : 0.045 0.184 1262 Planarity : 0.005 0.055 1425 Dihedral : 5.127 30.925 1130 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.97 % Favored : 91.84 % Rotamer: Outliers : 2.36 % Allowed : 21.55 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.71 (0.27), residues: 1030 helix: -1.66 (0.58), residues: 63 sheet: -0.66 (0.28), residues: 379 loop : -1.40 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.021 0.001 TYR E 495 PHE 0.027 0.002 PHE C 68 TRP 0.021 0.002 TRP C 36 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8199) covalent geometry : angle 0.70256 / 0.35 (11171) SS BOND : bond 0.00418 / 0.21 ( 10) SS BOND : angle 1.18558 / 0.67 ( 20) hydrogen bonds : bond 0.02895 / 1.92 ( 205) hydrogen bonds : angle 6.40343 / 4.48 ( 531) link_ALPHA1-6 : bond 0.00773 / 0.41 ( 1) link_ALPHA1-6 : angle 1.34252 / 0.74 ( 3) link_BETA1-4 : bond 0.00536 / 0.26 ( 2) link_BETA1-4 : angle 2.07080 / 1.05 ( 6) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.11425 / 0.64 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.31 seconds wall clock time: 40 minutes 4.33 seconds (2404.33 seconds total)