Starting phenix.real_space_refine on Wed Mar 4 02:37:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdz_14678/03_2026/7zdz_14678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdz_14678/03_2026/7zdz_14678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zdz_14678/03_2026/7zdz_14678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdz_14678/03_2026/7zdz_14678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zdz_14678/03_2026/7zdz_14678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdz_14678/03_2026/7zdz_14678.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Sr 2 13.11 5 K 1 8.98 5 S 79 5.16 5 C 6687 2.51 5 N 1736 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10369 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2611 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2575 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2572 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain: "D" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2608 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' SR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.20 Number of scatterers: 10369 At special positions: 0 Unit cell: (99.76, 96.32, 132.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sr 2 37.98 K 1 19.00 S 79 16.00 O 1864 8.00 N 1736 7.00 C 6687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 154 " 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 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 445.8 milliseconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 19 sheets defined 31.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 154 through 185 removed outlier: 3.909A pdb=" N LYS A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 3.542A pdb=" N ILE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.910A pdb=" N TYR A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 4.212A pdb=" N LYS B 64 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.688A pdb=" N ILE B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 115 removed outlier: 3.849A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 141 Processing helix chain 'B' and resid 154 through 185 Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.535A pdb=" N ILE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 111 Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.832A pdb=" N ALA C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 181 removed outlier: 3.643A pdb=" N VAL C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.392A pdb=" N ARG C 343 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 110 removed outlier: 4.712A pdb=" N THR D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS D 76 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG D 80 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TRP D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ARG D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL D 86 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 129 through 141 Processing helix chain 'D' and resid 154 through 184 removed outlier: 4.169A pdb=" N VAL D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 357 through 364 removed outlier: 3.941A pdb=" N LEU D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.703A pdb=" N TRP A 212 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.587A pdb=" N ARG A 235 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 293 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 313 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.610A pdb=" N GLN B 57 " --> pdb=" O VAL C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 249 removed outlier: 5.201A pdb=" N ARG B 235 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 333 Processing sheet with id=AB2, first strand: chain 'C' and resid 194 through 195 removed outlier: 3.551A pdb=" N VAL C 200 " --> pdb=" O MET C 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.080A pdb=" N LEU C 245 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 233 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN C 247 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 231 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP C 249 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA C 229 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU C 224 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N MET C 301 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 299 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AB6, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.908A pdb=" N VAL D 200 " --> pdb=" O MET D 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 193 through 195 Processing sheet with id=AB8, first strand: chain 'D' and resid 242 through 249 removed outlier: 5.281A pdb=" N ARG D 235 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 293 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 294 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 315 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 313 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AC1, first strand: chain 'D' and resid 324 through 325 389 hydrogen bonds defined for protein. 1086 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: 1.33 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3293 1.34 - 1.46: 1831 1.46 - 1.58: 5368 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 10603 Sorted by residual: bond pdb=" CA TYR C 68 " pdb=" C TYR C 68 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.34e-02 5.57e+03 1.65e+01 bond pdb=" N ILE C 72 " pdb=" CA ILE C 72 " ideal model delta sigma weight residual 1.459 1.413 0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" CA ASP C 71 " pdb=" C ASP C 71 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.80e+00 bond pdb=" CA LEU C 69 " pdb=" C LEU C 69 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 8.86e+00 bond pdb=" CA TYR D 280 " pdb=" C TYR D 280 " ideal model delta sigma weight residual 1.522 1.485 0.038 1.37e-02 5.33e+03 7.62e+00 ... (remaining 10598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 14188 3.20 - 6.39: 141 6.39 - 9.59: 17 9.59 - 12.78: 6 12.78 - 15.98: 1 Bond angle restraints: 14353 Sorted by residual: angle pdb=" N ASN A 127 " pdb=" CA ASN A 127 " pdb=" C ASN A 127 " ideal model delta sigma weight residual 112.03 96.05 15.98 1.31e+00 5.83e-01 1.49e+02 angle pdb=" N LYS B 334 " pdb=" CA LYS B 334 " pdb=" C LYS B 334 " ideal model delta sigma weight residual 108.67 98.31 10.36 1.67e+00 3.59e-01 3.85e+01 angle pdb=" N HIS C 335 " pdb=" CA HIS C 335 " pdb=" C HIS C 335 " ideal model delta sigma weight residual 113.17 105.47 7.70 1.26e+00 6.30e-01 3.73e+01 angle pdb=" N VAL D 264 " pdb=" CA VAL D 264 " pdb=" C VAL D 264 " ideal model delta sigma weight residual 113.71 108.30 5.41 9.50e-01 1.11e+00 3.25e+01 angle pdb=" C ILE C 72 " pdb=" N PHE C 73 " pdb=" CA PHE C 73 " ideal model delta sigma weight residual 121.54 110.92 10.62 1.91e+00 2.74e-01 3.09e+01 ... (remaining 14348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 5502 17.00 - 33.99: 619 33.99 - 50.99: 136 50.99 - 67.99: 15 67.99 - 84.98: 11 Dihedral angle restraints: 6283 sinusoidal: 2506 harmonic: 3777 Sorted by residual: dihedral pdb=" CB CYS C 122 " pdb=" SG CYS C 122 " pdb=" SG CYS C 154 " pdb=" CB CYS C 154 " ideal model delta sinusoidal sigma weight residual 93.00 27.40 65.60 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS D 122 " pdb=" SG CYS D 122 " pdb=" SG CYS D 154 " pdb=" CB CYS D 154 " ideal model delta sinusoidal sigma weight residual 93.00 143.20 -50.20 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA TYR C 336 " pdb=" C TYR C 336 " pdb=" N TYR C 337 " pdb=" CA TYR C 337 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1205 0.049 - 0.098: 313 0.098 - 0.147: 85 0.147 - 0.196: 6 0.196 - 0.245: 7 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA ARG C 312 " pdb=" N ARG C 312 " pdb=" C ARG C 312 " pdb=" CB ARG C 312 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLU B 303 " pdb=" N GLU B 303 " pdb=" C GLU B 303 " pdb=" CB GLU B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ARG A 312 " pdb=" N ARG A 312 " pdb=" C ARG A 312 " pdb=" CB ARG A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1613 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 96 " -0.029 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP C 96 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP C 96 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 96 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 96 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 96 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 96 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 96 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 333 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C GLU C 333 " -0.046 2.00e-02 2.50e+03 pdb=" O GLU C 333 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS C 334 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 96 " -0.021 2.00e-02 2.50e+03 1.68e-02 7.05e+00 pdb=" CG TRP D 96 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 96 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 96 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 96 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 96 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 96 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 96 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 96 " 0.002 2.00e-02 2.50e+03 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 2205 2.78 - 3.37: 11861 3.37 - 3.96: 18161 3.96 - 4.55: 23246 4.55 - 5.14: 35191 Nonbonded interactions: 90664 Sorted by model distance: nonbonded pdb=" O ARG C 67 " pdb=" C TYR C 68 " model vdw 2.192 3.270 nonbonded pdb=" O ARG D 325 " pdb=" OG1 THR D 347 " model vdw 2.228 3.040 nonbonded pdb=" NH2 ARG D 46 " pdb=" OD2 ASP D 51 " model vdw 2.261 3.120 nonbonded pdb=" O ILE C 137 " pdb=" OG1 THR C 141 " model vdw 2.262 3.040 nonbonded pdb=" O VAL C 61 " pdb=" OH TYR D 341 " model vdw 2.281 3.040 ... (remaining 90659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 363) selection = (chain 'B' and resid 44 through 363) selection = (chain 'C' and resid 44 through 363) selection = (chain 'D' and resid 44 through 363) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 : 0.003 0.054 10607 Z= 0.209 Angle : 0.860 15.979 14361 Z= 0.503 Chirality : 0.048 0.245 1616 Planarity : 0.004 0.032 1808 Dihedral : 15.046 84.983 3823 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.14 % Favored : 88.55 % Rotamer: Outliers : 0.35 % Allowed : 1.14 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.61 (0.23), residues: 1284 helix: 1.13 (0.27), residues: 367 sheet: -1.09 (0.39), residues: 157 loop : -2.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 312 TYR 0.019 0.001 TYR C 337 PHE 0.029 0.002 PHE D 103 TRP 0.065 0.002 TRP C 96 HIS 0.008 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00337 (10603) covalent geometry : angle 0.85984 (14353) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.58953 ( 8) hydrogen bonds : bond 0.14555 ( 385) hydrogen bonds : angle 6.12263 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 259 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 211 MET cc_start: 0.3964 (ttm) cc_final: 0.3406 (ttm) REVERT: A 247 GLN cc_start: 0.7961 (mp10) cc_final: 0.7543 (mp10) REVERT: A 295 VAL cc_start: 0.9078 (t) cc_final: 0.8826 (m) REVERT: B 134 LEU cc_start: 0.8661 (tt) cc_final: 0.8425 (tt) REVERT: B 360 ASP cc_start: 0.8541 (m-30) cc_final: 0.8276 (m-30) REVERT: C 211 MET cc_start: 0.4424 (ptm) cc_final: 0.3493 (ptm) REVERT: C 310 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 312 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8621 (mtt180) REVERT: D 103 PHE cc_start: 0.7728 (m-80) cc_final: 0.7405 (m-80) REVERT: D 160 MET cc_start: 0.7867 (ttt) cc_final: 0.7547 (tpt) REVERT: D 285 GLN cc_start: 0.8382 (pp30) cc_final: 0.8007 (pp30) REVERT: D 299 GLU cc_start: 0.7847 (pt0) cc_final: 0.7631 (pp20) REVERT: D 341 TYR cc_start: 0.5369 (p90) cc_final: 0.5124 (p90) outliers start: 4 outliers final: 1 residues processed: 262 average time/residue: 0.0744 time to fit residues: 29.5253 Evaluate side-chains 228 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 60 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142313 restraints weight = 22684.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144599 restraints weight = 17484.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147011 restraints weight = 13794.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148342 restraints weight = 10518.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148590 restraints weight = 9775.595| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10607 Z= 0.223 Angle : 0.700 6.524 14361 Z= 0.379 Chirality : 0.047 0.150 1616 Planarity : 0.004 0.041 1808 Dihedral : 5.677 29.193 1397 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.08 % Favored : 86.76 % Rotamer: Outliers : 0.09 % Allowed : 9.68 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.89 (0.23), residues: 1284 helix: 0.76 (0.26), residues: 365 sheet: -1.27 (0.39), residues: 163 loop : -2.42 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 46 TYR 0.018 0.002 TYR C 337 PHE 0.031 0.002 PHE D 133 TRP 0.046 0.002 TRP C 96 HIS 0.010 0.002 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00489 (10603) covalent geometry : angle 0.70014 (14353) SS BOND : bond 0.00667 ( 4) SS BOND : angle 0.45669 ( 8) hydrogen bonds : bond 0.05206 ( 385) hydrogen bonds : angle 5.22749 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7906 (mmp-170) cc_final: 0.6995 (mmt-90) REVERT: A 53 HIS cc_start: 0.6577 (t-90) cc_final: 0.6317 (t-170) REVERT: A 247 GLN cc_start: 0.8160 (mp10) cc_final: 0.7672 (mp10) REVERT: B 134 LEU cc_start: 0.8977 (tt) cc_final: 0.8756 (tp) REVERT: B 360 ASP cc_start: 0.8657 (m-30) cc_final: 0.8320 (m-30) REVERT: C 211 MET cc_start: 0.5144 (ptm) cc_final: 0.4418 (ptm) REVERT: C 216 ASN cc_start: 0.7857 (m110) cc_final: 0.7583 (m-40) REVERT: D 211 MET cc_start: 0.7021 (ptp) cc_final: 0.6654 (ptp) REVERT: D 285 GLN cc_start: 0.8420 (pp30) cc_final: 0.7984 (pp30) REVERT: D 331 PHE cc_start: 0.7911 (t80) cc_final: 0.7697 (t80) REVERT: D 336 TYR cc_start: 0.7416 (m-10) cc_final: 0.7085 (m-10) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.0736 time to fit residues: 28.6785 Evaluate side-chains 212 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 ASN C 190 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.174450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140621 restraints weight = 22797.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143574 restraints weight = 16609.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145935 restraints weight = 12983.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147053 restraints weight = 10043.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147365 restraints weight = 9318.692| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10607 Z= 0.224 Angle : 0.710 8.139 14361 Z= 0.384 Chirality : 0.047 0.171 1616 Planarity : 0.004 0.032 1808 Dihedral : 5.868 27.583 1397 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.86 % Favored : 85.98 % Rotamer: Outliers : 0.09 % Allowed : 8.45 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.22), residues: 1284 helix: 0.39 (0.25), residues: 372 sheet: -1.32 (0.40), residues: 160 loop : -2.58 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 44 TYR 0.021 0.002 TYR C 337 PHE 0.033 0.003 PHE D 103 TRP 0.047 0.002 TRP D 96 HIS 0.010 0.002 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00496 (10603) covalent geometry : angle 0.71037 (14353) SS BOND : bond 0.00328 ( 4) SS BOND : angle 0.39459 ( 8) hydrogen bonds : bond 0.05188 ( 385) hydrogen bonds : angle 5.33130 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8746 (tm-30) REVERT: B 360 ASP cc_start: 0.8627 (m-30) cc_final: 0.8399 (m-30) REVERT: C 66 GLN cc_start: 0.6647 (tp40) cc_final: 0.6390 (tm-30) REVERT: C 189 ARG cc_start: 0.7149 (ptp90) cc_final: 0.6646 (ttt180) REVERT: C 200 VAL cc_start: 0.8054 (p) cc_final: 0.7829 (p) REVERT: C 211 MET cc_start: 0.5490 (ptm) cc_final: 0.4934 (ptm) REVERT: C 216 ASN cc_start: 0.8027 (m110) cc_final: 0.7424 (m-40) REVERT: C 310 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8078 (tm-30) REVERT: D 103 PHE cc_start: 0.7908 (m-80) cc_final: 0.7659 (m-80) REVERT: D 211 MET cc_start: 0.7096 (ptp) cc_final: 0.6764 (ptp) REVERT: D 285 GLN cc_start: 0.8500 (pp30) cc_final: 0.8048 (pp30) REVERT: D 331 PHE cc_start: 0.7967 (t80) cc_final: 0.7731 (t80) REVERT: D 341 TYR cc_start: 0.5246 (p90) cc_final: 0.4888 (p90) outliers start: 1 outliers final: 1 residues processed: 273 average time/residue: 0.0830 time to fit residues: 33.5084 Evaluate side-chains 230 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 221 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147068 restraints weight = 22355.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149929 restraints weight = 16560.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.152567 restraints weight = 12527.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.154727 restraints weight = 9636.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154969 restraints weight = 8541.172| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10607 Z= 0.132 Angle : 0.645 8.652 14361 Z= 0.343 Chirality : 0.046 0.164 1616 Planarity : 0.003 0.045 1808 Dihedral : 5.322 28.241 1397 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.46 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.87 (0.23), residues: 1284 helix: 0.84 (0.26), residues: 370 sheet: -1.17 (0.39), residues: 173 loop : -2.50 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 44 TYR 0.019 0.001 TYR D 341 PHE 0.030 0.002 PHE B 159 TRP 0.030 0.001 TRP D 96 HIS 0.009 0.001 HIS D 271 Details of bonding type rmsd covalent geometry : bond 0.00286 (10603) covalent geometry : angle 0.64486 (14353) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.77084 ( 8) hydrogen bonds : bond 0.04346 ( 385) hydrogen bonds : angle 4.89332 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7646 (mmp-170) cc_final: 0.6567 (mmt-90) REVERT: A 164 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8780 (tm-30) REVERT: B 164 GLN cc_start: 0.9121 (pp30) cc_final: 0.8910 (pp30) REVERT: B 341 TYR cc_start: 0.7552 (m-80) cc_final: 0.7246 (m-80) REVERT: B 360 ASP cc_start: 0.8673 (m-30) cc_final: 0.8300 (m-30) REVERT: C 66 GLN cc_start: 0.6586 (tp40) cc_final: 0.6206 (tm-30) REVERT: C 189 ARG cc_start: 0.7054 (ptp90) cc_final: 0.6528 (ttt180) REVERT: C 200 VAL cc_start: 0.7808 (p) cc_final: 0.7554 (p) REVERT: C 211 MET cc_start: 0.5155 (ptm) cc_final: 0.4561 (ptm) REVERT: C 216 ASN cc_start: 0.7942 (m110) cc_final: 0.7371 (m-40) REVERT: C 310 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 211 MET cc_start: 0.7016 (ptp) cc_final: 0.6655 (ptp) REVERT: D 285 GLN cc_start: 0.8455 (pp30) cc_final: 0.8008 (pp30) REVERT: D 341 TYR cc_start: 0.5324 (p90) cc_final: 0.5069 (p90) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.0767 time to fit residues: 32.8215 Evaluate side-chains 241 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 0.0370 chunk 76 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 0.0070 chunk 118 optimal weight: 20.0000 overall best weight: 4.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 230 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.176043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142400 restraints weight = 22360.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145398 restraints weight = 16255.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147401 restraints weight = 12765.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149377 restraints weight = 9849.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149378 restraints weight = 8838.610| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10607 Z= 0.195 Angle : 0.698 8.449 14361 Z= 0.375 Chirality : 0.047 0.202 1616 Planarity : 0.004 0.051 1808 Dihedral : 5.765 27.769 1397 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.10 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.23), residues: 1284 helix: 0.44 (0.25), residues: 372 sheet: -1.17 (0.40), residues: 165 loop : -2.55 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 44 TYR 0.018 0.002 TYR B 337 PHE 0.047 0.002 PHE D 133 TRP 0.051 0.002 TRP D 96 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00432 (10603) covalent geometry : angle 0.69849 (14353) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.52152 ( 8) hydrogen bonds : bond 0.04894 ( 385) hydrogen bonds : angle 5.14185 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ASP cc_start: 0.8620 (m-30) cc_final: 0.8215 (m-30) REVERT: C 66 GLN cc_start: 0.6358 (tp40) cc_final: 0.5980 (tm-30) REVERT: C 103 PHE cc_start: 0.7704 (m-80) cc_final: 0.7203 (m-80) REVERT: C 164 GLN cc_start: 0.9038 (pp30) cc_final: 0.8780 (pp30) REVERT: C 189 ARG cc_start: 0.6927 (ptp90) cc_final: 0.6345 (ttt180) REVERT: C 200 VAL cc_start: 0.8073 (p) cc_final: 0.7786 (p) REVERT: C 211 MET cc_start: 0.5326 (ptm) cc_final: 0.4844 (ptm) REVERT: C 216 ASN cc_start: 0.8054 (m110) cc_final: 0.7775 (m-40) REVERT: D 211 MET cc_start: 0.7217 (ptp) cc_final: 0.6833 (ptp) REVERT: D 285 GLN cc_start: 0.8490 (pp30) cc_final: 0.8028 (pp30) REVERT: D 310 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 331 PHE cc_start: 0.7937 (t80) cc_final: 0.7723 (t80) REVERT: D 341 TYR cc_start: 0.5449 (p90) cc_final: 0.5098 (p90) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.0799 time to fit residues: 32.9589 Evaluate side-chains 229 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 95 optimal weight: 40.0000 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 119 optimal weight: 0.0270 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.185219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.151624 restraints weight = 22472.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155332 restraints weight = 16425.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157781 restraints weight = 12181.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160408 restraints weight = 9173.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160209 restraints weight = 8106.174| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10607 Z= 0.119 Angle : 0.650 9.913 14361 Z= 0.337 Chirality : 0.045 0.171 1616 Planarity : 0.004 0.056 1808 Dihedral : 5.063 28.004 1397 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.53 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.23), residues: 1284 helix: 1.05 (0.26), residues: 370 sheet: -0.77 (0.40), residues: 160 loop : -2.51 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 46 TYR 0.021 0.001 TYR D 341 PHE 0.026 0.002 PHE A 88 TRP 0.038 0.002 TRP D 96 HIS 0.005 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00245 (10603) covalent geometry : angle 0.64995 (14353) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.47453 ( 8) hydrogen bonds : bond 0.04001 ( 385) hydrogen bonds : angle 4.62920 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8002 (mp10) cc_final: 0.7481 (mp10) REVERT: B 360 ASP cc_start: 0.8683 (m-30) cc_final: 0.8345 (m-30) REVERT: C 66 GLN cc_start: 0.6595 (tp40) cc_final: 0.6163 (tm-30) REVERT: C 103 PHE cc_start: 0.7605 (m-80) cc_final: 0.7290 (m-80) REVERT: C 164 GLN cc_start: 0.8959 (pp30) cc_final: 0.8726 (pp30) REVERT: C 211 MET cc_start: 0.5094 (ptm) cc_final: 0.4424 (ptm) REVERT: C 216 ASN cc_start: 0.7907 (m110) cc_final: 0.7379 (m-40) REVERT: D 279 LEU cc_start: 0.8843 (mt) cc_final: 0.8599 (mt) REVERT: D 285 GLN cc_start: 0.8409 (pp30) cc_final: 0.7981 (pp30) REVERT: D 310 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8046 (tm-30) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.0788 time to fit residues: 34.3218 Evaluate side-chains 239 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS A 230 GLN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS C 190 ASN C 271 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143418 restraints weight = 22729.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146581 restraints weight = 16930.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148705 restraints weight = 13124.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150183 restraints weight = 10188.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150566 restraints weight = 9201.989| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10607 Z= 0.199 Angle : 0.710 8.917 14361 Z= 0.376 Chirality : 0.047 0.219 1616 Planarity : 0.004 0.051 1808 Dihedral : 5.620 28.078 1397 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.71 % Favored : 86.14 % Rotamer: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.23), residues: 1284 helix: 0.62 (0.25), residues: 367 sheet: -1.03 (0.39), residues: 170 loop : -2.55 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 44 TYR 0.017 0.002 TYR B 337 PHE 0.035 0.002 PHE D 133 TRP 0.030 0.002 TRP D 96 HIS 0.019 0.002 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00445 (10603) covalent geometry : angle 0.71027 (14353) SS BOND : bond 0.00383 ( 4) SS BOND : angle 0.62532 ( 8) hydrogen bonds : bond 0.04702 ( 385) hydrogen bonds : angle 4.99853 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7735 (mmp-170) cc_final: 0.6618 (mmt-90) REVERT: A 183 MET cc_start: 0.7690 (mmm) cc_final: 0.7345 (mtt) REVERT: B 134 LEU cc_start: 0.8872 (tt) cc_final: 0.8639 (tt) REVERT: B 293 GLU cc_start: 0.7985 (tp30) cc_final: 0.7246 (tm-30) REVERT: B 360 ASP cc_start: 0.8605 (m-30) cc_final: 0.8222 (m-30) REVERT: C 66 GLN cc_start: 0.6424 (tp40) cc_final: 0.6100 (tm-30) REVERT: C 103 PHE cc_start: 0.7517 (m-80) cc_final: 0.7138 (m-80) REVERT: C 160 MET cc_start: 0.8174 (ttt) cc_final: 0.7904 (ttm) REVERT: C 211 MET cc_start: 0.5310 (ptm) cc_final: 0.4671 (ptm) REVERT: C 216 ASN cc_start: 0.8022 (m110) cc_final: 0.7458 (m-40) REVERT: D 211 MET cc_start: 0.7086 (ptp) cc_final: 0.6697 (ptp) REVERT: D 285 GLN cc_start: 0.8448 (pp30) cc_final: 0.7995 (pp30) REVERT: D 310 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7919 (tm-30) outliers start: 1 outliers final: 1 residues processed: 273 average time/residue: 0.0783 time to fit residues: 32.5934 Evaluate side-chains 224 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 73 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 21 optimal weight: 0.0020 chunk 23 optimal weight: 0.0470 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 0.0030 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 335 HIS C 110 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.182799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149241 restraints weight = 22276.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.152957 restraints weight = 16371.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.155496 restraints weight = 12046.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.157321 restraints weight = 9093.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.157666 restraints weight = 8092.364| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10607 Z= 0.130 Angle : 0.687 9.720 14361 Z= 0.355 Chirality : 0.046 0.157 1616 Planarity : 0.004 0.034 1808 Dihedral : 5.266 28.789 1397 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.07 % Favored : 87.77 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.23), residues: 1284 helix: 0.81 (0.26), residues: 371 sheet: -0.82 (0.39), residues: 164 loop : -2.50 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 44 TYR 0.027 0.001 TYR D 341 PHE 0.033 0.002 PHE D 92 TRP 0.061 0.002 TRP D 96 HIS 0.009 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00277 (10603) covalent geometry : angle 0.68751 (14353) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.47903 ( 8) hydrogen bonds : bond 0.04293 ( 385) hydrogen bonds : angle 4.75632 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 GLU cc_start: 0.5656 (tp30) cc_final: 0.5422 (tp30) REVERT: B 134 LEU cc_start: 0.8888 (tt) cc_final: 0.8608 (tp) REVERT: B 360 ASP cc_start: 0.8633 (m-30) cc_final: 0.8275 (m-30) REVERT: C 66 GLN cc_start: 0.6683 (tp40) cc_final: 0.6307 (tm-30) REVERT: C 211 MET cc_start: 0.5188 (ptm) cc_final: 0.4586 (ptm) REVERT: C 216 ASN cc_start: 0.7948 (m110) cc_final: 0.7398 (m-40) REVERT: D 211 MET cc_start: 0.6921 (ptp) cc_final: 0.6485 (ptp) REVERT: D 285 GLN cc_start: 0.8399 (pp30) cc_final: 0.8008 (pp30) REVERT: D 310 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8026 (tm-30) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.0724 time to fit residues: 31.1225 Evaluate side-chains 229 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 0.0040 chunk 72 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN C 190 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.181969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148208 restraints weight = 22096.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.151853 restraints weight = 16040.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154037 restraints weight = 11920.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156635 restraints weight = 9134.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156443 restraints weight = 7987.398| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10607 Z= 0.134 Angle : 0.681 9.631 14361 Z= 0.355 Chirality : 0.046 0.150 1616 Planarity : 0.004 0.034 1808 Dihedral : 5.238 27.826 1397 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.46 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.23), residues: 1284 helix: 0.86 (0.26), residues: 370 sheet: -0.82 (0.38), residues: 175 loop : -2.51 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 44 TYR 0.020 0.001 TYR B 337 PHE 0.041 0.002 PHE B 159 TRP 0.047 0.002 TRP D 96 HIS 0.009 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00292 (10603) covalent geometry : angle 0.68131 (14353) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.49969 ( 8) hydrogen bonds : bond 0.04364 ( 385) hydrogen bonds : angle 4.76461 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 GLU cc_start: 0.5700 (tp30) cc_final: 0.5466 (tp30) REVERT: B 164 GLN cc_start: 0.9177 (pp30) cc_final: 0.8908 (pp30) REVERT: B 360 ASP cc_start: 0.8690 (m-30) cc_final: 0.8298 (m-30) REVERT: C 66 GLN cc_start: 0.6791 (tp40) cc_final: 0.6364 (tm-30) REVERT: C 92 PHE cc_start: 0.7645 (t80) cc_final: 0.7425 (t80) REVERT: C 211 MET cc_start: 0.5250 (ptm) cc_final: 0.4670 (ptm) REVERT: C 216 ASN cc_start: 0.7959 (m110) cc_final: 0.7512 (m-40) REVERT: D 285 GLN cc_start: 0.8381 (pp30) cc_final: 0.8012 (pp30) REVERT: D 310 GLN cc_start: 0.8262 (tm-30) cc_final: 0.8027 (tm-30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.0739 time to fit residues: 30.8117 Evaluate side-chains 233 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 92 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 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 = 0.4282 r_free = 0.4282 target = 0.181273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147412 restraints weight = 22130.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151031 restraints weight = 16058.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.152981 restraints weight = 12135.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155262 restraints weight = 9436.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155796 restraints weight = 8134.473| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10607 Z= 0.142 Angle : 0.690 9.898 14361 Z= 0.358 Chirality : 0.046 0.163 1616 Planarity : 0.004 0.038 1808 Dihedral : 5.291 27.979 1397 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.93 % Favored : 86.92 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.23), residues: 1284 helix: 0.89 (0.26), residues: 370 sheet: -0.72 (0.39), residues: 164 loop : -2.49 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 44 TYR 0.017 0.001 TYR B 337 PHE 0.038 0.002 PHE B 159 TRP 0.057 0.002 TRP C 96 HIS 0.010 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00312 (10603) covalent geometry : angle 0.68978 (14353) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.48238 ( 8) hydrogen bonds : bond 0.04410 ( 385) hydrogen bonds : angle 4.76117 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 GLU cc_start: 0.5645 (tp30) cc_final: 0.5409 (tp30) REVERT: B 164 GLN cc_start: 0.9186 (pp30) cc_final: 0.8958 (pp30) REVERT: B 293 GLU cc_start: 0.7961 (tp30) cc_final: 0.7408 (tm-30) REVERT: B 360 ASP cc_start: 0.8605 (m-30) cc_final: 0.8279 (m-30) REVERT: C 66 GLN cc_start: 0.6917 (tp40) cc_final: 0.6480 (tm-30) REVERT: C 92 PHE cc_start: 0.7577 (t80) cc_final: 0.7184 (t80) REVERT: C 103 PHE cc_start: 0.7589 (m-80) cc_final: 0.7164 (m-80) REVERT: C 211 MET cc_start: 0.5274 (ptm) cc_final: 0.4669 (ptm) REVERT: C 216 ASN cc_start: 0.7992 (m110) cc_final: 0.7452 (m-40) REVERT: D 285 GLN cc_start: 0.8403 (pp30) cc_final: 0.8023 (pp30) REVERT: D 310 GLN cc_start: 0.8255 (tm-30) cc_final: 0.8007 (tm-30) REVERT: D 341 TYR cc_start: 0.5328 (p90) cc_final: 0.4918 (p90) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.0745 time to fit residues: 30.6559 Evaluate side-chains 228 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.179331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145289 restraints weight = 22523.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148719 restraints weight = 16323.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150893 restraints weight = 12281.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153233 restraints weight = 9394.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153098 restraints weight = 8383.998| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10607 Z= 0.166 Angle : 0.707 9.702 14361 Z= 0.370 Chirality : 0.047 0.151 1616 Planarity : 0.004 0.055 1808 Dihedral : 5.458 28.843 1397 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.40 % Favored : 86.45 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.23), residues: 1284 helix: 0.83 (0.26), residues: 370 sheet: -0.82 (0.40), residues: 164 loop : -2.52 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 44 TYR 0.019 0.002 TYR B 337 PHE 0.035 0.002 PHE B 159 TRP 0.086 0.002 TRP C 96 HIS 0.011 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00369 (10603) covalent geometry : angle 0.70712 (14353) SS BOND : bond 0.00321 ( 4) SS BOND : angle 0.50647 ( 8) hydrogen bonds : bond 0.04614 ( 385) hydrogen bonds : angle 4.81779 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.56 seconds wall clock time: 30 minutes 8.66 seconds (1808.66 seconds total)