Starting phenix.real_space_refine on Thu Jul 2 11:27:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8urq_42497/07_2026/8urq_42497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urq_42497/07_2026/8urq_42497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8urq_42497/07_2026/8urq_42497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urq_42497/07_2026/8urq_42497.map" model { file = "/net/cci-nas-00/data/ceres_data/8urq_42497/07_2026/8urq_42497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urq_42497/07_2026/8urq_42497.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.083 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 P 31 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 5378 2.51 5 N 1463 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8569 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 407 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1845 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2875 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2805 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 348} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 636 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.89, per 1000 atoms: 0.22 Number of scatterers: 8569 At special positions: 0 Unit cell: (69.16, 110.656, 135.128, 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) S 36 16.00 P 31 15.00 Mg 1 11.99 O 1660 8.00 N 1463 7.00 C 5378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 420.7 milliseconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 26.7% alpha, 12.1% beta 5 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.610A pdb=" N PHE F 17 " --> pdb=" O CYS F 13 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.624A pdb=" N SER F 28 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 29 " --> pdb=" O ARG F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 42 through 58 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 119 through 134 removed outlier: 3.824A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.534A pdb=" N GLN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 220 through 231 Processing helix chain 'B' and resid 236 through 241 removed outlier: 3.519A pdb=" N ILE B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 236 through 241' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 104 through 122 removed outlier: 3.535A pdb=" N CYS A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.606A pdb=" N ASN A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.787A pdb=" N VAL A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.605A pdb=" N TYR A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.626A pdb=" N LEU A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.631A pdb=" N ILE A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.784A pdb=" N ASP C 53 " --> pdb=" O ASN C 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.741A pdb=" N LEU B 47 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 49 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 146 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLU B 148 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.353A pdb=" N ARG A 25 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 70 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE A 27 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.512A pdb=" N THR A 128 " --> pdb=" O ILE A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.540A pdb=" N CYS A 208 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.602A pdb=" N LEU C 38 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 40 " --> pdb=" O TYR C 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 72 removed outlier: 3.957A pdb=" N HIS C 67 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.961A pdb=" N GLU C 110 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C 108 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.950A pdb=" N LEU C 141 " --> pdb=" O TRP C 153 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR C 150 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR C 178 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE C 152 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 210 through 211 removed outlier: 3.592A pdb=" N ILE C 211 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR C 221 " --> pdb=" O ILE C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 236 through 241 removed outlier: 3.507A pdb=" N SER C 238 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 248 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 260 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY C 272 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.620A pdb=" N SER C 298 " --> pdb=" O CYS C 307 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 307 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 306 " --> pdb=" O TRP C 318 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 357 through 362 removed outlier: 3.965A pdb=" N ASP C 359 " --> pdb=" O VAL C 382 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.52: 5914 1.52 - 1.85: 2888 1.85 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.85: 1 Bond restraints: 8803 Sorted by residual: bond pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 1.329 2.851 -1.522 1.40e-02 5.10e+03 1.18e+04 bond pdb=" CA PRO A 96 " pdb=" C PRO A 96 " ideal model delta sigma weight residual 1.526 1.479 0.047 9.80e-03 1.04e+04 2.27e+01 bond pdb=" N ASP C 18 " pdb=" CA ASP C 18 " ideal model delta sigma weight residual 1.457 1.516 -0.058 1.29e-02 6.01e+03 2.04e+01 bond pdb=" C GLY A 257 " pdb=" O GLY A 257 " ideal model delta sigma weight residual 1.232 1.188 0.044 1.03e-02 9.43e+03 1.85e+01 bond pdb=" C TYR A 292 " pdb=" O TYR A 292 " ideal model delta sigma weight residual 1.237 1.183 0.054 1.36e-02 5.41e+03 1.55e+01 ... (remaining 8798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.53: 12018 11.53 - 23.07: 2 23.07 - 34.60: 0 34.60 - 46.14: 1 46.14 - 57.67: 2 Bond angle restraints: 12023 Sorted by residual: angle pdb=" O LEU B 12 " pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 122.20 64.53 57.67 1.34e+00 5.57e-01 1.85e+03 angle pdb=" CA LEU B 12 " pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 117.06 169.95 -52.89 1.53e+00 4.27e-01 1.20e+03 angle pdb=" C LEU B 12 " pdb=" N SER B 28 " pdb=" CA SER B 28 " ideal model delta sigma weight residual 121.70 85.35 36.35 1.80e+00 3.09e-01 4.08e+02 angle pdb=" N ILE A 353 " pdb=" CA ILE A 353 " pdb=" C ILE A 353 " ideal model delta sigma weight residual 111.90 101.91 9.99 8.10e-01 1.52e+00 1.52e+02 angle pdb=" N LYS A 258 " pdb=" CA LYS A 258 " pdb=" C LYS A 258 " ideal model delta sigma weight residual 111.28 123.48 -12.20 1.09e+00 8.42e-01 1.25e+02 ... (remaining 12018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4120 17.38 - 34.75: 666 34.75 - 52.13: 308 52.13 - 69.50: 82 69.50 - 86.88: 18 Dihedral angle restraints: 5194 sinusoidal: 2287 harmonic: 2907 Sorted by residual: dihedral pdb=" CA MET A 253 " pdb=" C MET A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PRO B 247 " pdb=" C PRO B 247 " pdb=" N PRO B 248 " pdb=" CA PRO B 248 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C LYS A 258 " pdb=" N LYS A 258 " pdb=" CA LYS A 258 " pdb=" CB LYS A 258 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 5191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1287 0.103 - 0.206: 71 0.206 - 0.308: 9 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA LYS A 258 " pdb=" N LYS A 258 " pdb=" C LYS A 258 " pdb=" CB LYS A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA PHE F 22 " pdb=" N PHE F 22 " pdb=" C PHE F 22 " pdb=" CB PHE F 22 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLN A 343 " pdb=" N GLN A 343 " pdb=" C GLN A 343 " pdb=" CB GLN A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1365 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 12 " 0.052 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C LEU B 12 " -0.086 2.00e-02 2.50e+03 pdb=" O LEU B 12 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 28 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC D 41 " -0.049 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" N1 DC D 41 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC D 41 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DC D 41 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC D 41 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC D 41 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC D 41 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC D 41 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC D 41 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 169 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A 170 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.047 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 33 2.40 - 3.02: 4835 3.02 - 3.65: 12661 3.65 - 4.27: 18672 4.27 - 4.90: 31171 Nonbonded interactions: 67372 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb="MG MG A 501 " model vdw 1.769 2.170 nonbonded pdb=" OD2 ASP A 290 " pdb="MG MG A 501 " model vdw 1.915 2.170 nonbonded pdb=" O HIS A 97 " pdb=" ND1 HIS A 97 " model vdw 2.129 3.120 nonbonded pdb=" O GLU A 235 " pdb=" OG1 THR A 239 " model vdw 2.225 3.040 nonbonded pdb=" O THR B 9 " pdb=" OG1 THR B 9 " model vdw 2.229 3.040 ... (remaining 67367 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.017 1.522 8803 Z= 1.207 Angle : 1.234 57.670 12023 Z= 0.809 Chirality : 0.055 0.514 1368 Planarity : 0.006 0.087 1407 Dihedral : 21.281 86.876 3290 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.81 % Favored : 88.88 % Rotamer: Outliers : 4.61 % Allowed : 32.25 % Favored : 63.15 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.94 % 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: -3.76 (0.24), residues: 953 helix: -1.21 (0.32), residues: 263 sheet: -3.08 (0.35), residues: 180 loop : -3.04 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.031 0.002 TYR C 56 PHE 0.026 0.002 PHE C 288 TRP 0.017 0.002 TRP C 129 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.01702 / 1.21 ( 8803) covalent geometry : angle 1.23355 / 0.81 (12023) hydrogen bonds : bond 0.23323 / 15.70 ( 202) hydrogen bonds : angle 9.51120 / 6.87 ( 565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.195 Fit side-chains REVERT: F 15 GLN cc_start: 0.6236 (OUTLIER) cc_final: 0.5570 (pp30) REVERT: F 21 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: F 40 ARG cc_start: 0.7241 (tpp80) cc_final: 0.7007 (mtp85) REVERT: A 183 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: A 199 LYS cc_start: 0.7459 (pttt) cc_final: 0.7242 (ptmt) REVERT: A 200 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6225 (mt0) REVERT: A 206 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7709 (mttp) REVERT: A 214 GLN cc_start: 0.6909 (tp-100) cc_final: 0.6469 (mp10) REVERT: C 18 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.5735 (p0) REVERT: C 295 MET cc_start: 0.7044 (mmt) cc_final: 0.6161 (mmm) outliers start: 41 outliers final: 23 residues processed: 158 average time/residue: 0.0988 time to fit residues: 20.7038 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 123 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 86 HIS A 101 HIS A 102 GLN A 144 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.215590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.184856 restraints weight = 11092.004| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 2.34 r_work: 0.4199 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8803 Z= 0.146 Angle : 0.699 13.604 12023 Z= 0.367 Chirality : 0.046 0.273 1368 Planarity : 0.005 0.056 1407 Dihedral : 19.719 87.045 1457 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 6.63 % Allowed : 28.09 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.46 (0.25), residues: 955 helix: -0.90 (0.32), residues: 259 sheet: -2.83 (0.33), residues: 193 loop : -2.89 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 163 TYR 0.015 0.001 TYR A 300 PHE 0.012 0.001 PHE A 91 TRP 0.013 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 8803) covalent geometry : angle 0.69867 / 0.37 (12023) hydrogen bonds : bond 0.04941 / 2.95 ( 202) hydrogen bonds : angle 6.01381 / 4.45 ( 565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 108 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 15 GLN cc_start: 0.5862 (OUTLIER) cc_final: 0.5160 (pp30) REVERT: F 41 ILE cc_start: 0.8003 (mt) cc_final: 0.7364 (tt) REVERT: B 144 TYR cc_start: 0.6337 (m-10) cc_final: 0.5983 (m-10) REVERT: A 267 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6968 (tp) REVERT: C 21 SER cc_start: 0.7910 (m) cc_final: 0.7660 (m) REVERT: C 295 MET cc_start: 0.6915 (mmt) cc_final: 0.5964 (mmt) REVERT: C 343 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.4777 (tt) outliers start: 59 outliers final: 33 residues processed: 159 average time/residue: 0.0900 time to fit residues: 19.3428 Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS A 370 ASN C 43 ASN C 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.215809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.185672 restraints weight = 10918.198| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 2.35 r_work: 0.4206 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8803 Z= 0.123 Angle : 0.624 7.381 12023 Z= 0.329 Chirality : 0.044 0.197 1368 Planarity : 0.004 0.049 1407 Dihedral : 19.254 85.372 1416 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.83 % Allowed : 29.66 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.25), residues: 955 helix: -0.56 (0.32), residues: 259 sheet: -2.76 (0.32), residues: 219 loop : -2.83 (0.24), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.015 0.002 TYR A 245 PHE 0.028 0.001 PHE B 63 TRP 0.015 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8803) covalent geometry : angle 0.62395 / 0.33 (12023) hydrogen bonds : bond 0.04093 / 2.44 ( 202) hydrogen bonds : angle 5.57057 / 4.16 ( 565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.195 Fit side-chains REVERT: F 41 ILE cc_start: 0.7742 (mt) cc_final: 0.7163 (tt) REVERT: B 144 TYR cc_start: 0.6275 (m-10) cc_final: 0.5909 (m-10) REVERT: A 64 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6567 (tm-30) REVERT: C 21 SER cc_start: 0.7896 (m) cc_final: 0.7644 (m) REVERT: C 295 MET cc_start: 0.6940 (mmt) cc_final: 0.5997 (mmt) REVERT: C 343 LEU cc_start: 0.5226 (OUTLIER) cc_final: 0.4728 (tt) outliers start: 43 outliers final: 28 residues processed: 142 average time/residue: 0.0826 time to fit residues: 16.1718 Evaluate side-chains 123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.217308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.184325 restraints weight = 11285.992| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.46 r_work: 0.4138 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8803 Z= 0.161 Angle : 0.649 7.157 12023 Z= 0.342 Chirality : 0.045 0.204 1368 Planarity : 0.004 0.048 1407 Dihedral : 19.166 87.989 1412 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 5.96 % Allowed : 29.33 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.19 (0.25), residues: 955 helix: -0.59 (0.32), residues: 265 sheet: -2.67 (0.33), residues: 207 loop : -2.78 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.022 0.002 TYR A 300 PHE 0.021 0.002 PHE B 63 TRP 0.016 0.001 TRP C 129 HIS 0.008 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8803) covalent geometry : angle 0.64907 / 0.34 (12023) hydrogen bonds : bond 0.03820 / 2.34 ( 202) hydrogen bonds : angle 5.38645 / 4.04 ( 565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 93 time to evaluate : 0.223 Fit side-chains REVERT: F 41 ILE cc_start: 0.7529 (mt) cc_final: 0.7098 (tt) REVERT: B 74 GLN cc_start: 0.3143 (OUTLIER) cc_final: 0.2854 (pp30) REVERT: B 144 TYR cc_start: 0.6373 (m-10) cc_final: 0.5981 (m-10) REVERT: A 64 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 90 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6670 (t70) REVERT: A 299 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7336 (t0) REVERT: C 21 SER cc_start: 0.8079 (m) cc_final: 0.7811 (m) REVERT: C 81 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5459 (tt) REVERT: C 295 MET cc_start: 0.7010 (mmt) cc_final: 0.6086 (mmt) outliers start: 53 outliers final: 35 residues processed: 140 average time/residue: 0.0909 time to fit residues: 17.5654 Evaluate side-chains 128 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 HIS A 246 HIS A 323 GLN C 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.211030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177263 restraints weight = 11254.851| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.40 r_work: 0.4003 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8803 Z= 0.266 Angle : 0.762 8.903 12023 Z= 0.402 Chirality : 0.049 0.177 1368 Planarity : 0.005 0.049 1407 Dihedral : 19.341 88.688 1407 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 6.40 % Allowed : 29.78 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.47 (0.25), residues: 955 helix: -0.97 (0.31), residues: 261 sheet: -2.74 (0.34), residues: 203 loop : -2.89 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 26 TYR 0.034 0.003 TYR A 300 PHE 0.023 0.002 PHE B 176 TRP 0.019 0.002 TRP C 129 HIS 0.015 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 ( 8803) covalent geometry : angle 0.76163 / 0.40 (12023) hydrogen bonds : bond 0.04667 / 2.89 ( 202) hydrogen bonds : angle 5.77833 / 4.34 ( 565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 104 time to evaluate : 0.260 Fit side-chains REVERT: F 41 ILE cc_start: 0.7698 (mt) cc_final: 0.7293 (tt) REVERT: B 35 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6797 (tpt170) REVERT: B 114 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8188 (tttm) REVERT: B 144 TYR cc_start: 0.6532 (m-10) cc_final: 0.6144 (m-10) REVERT: A 24 ARG cc_start: 0.6904 (mtt180) cc_final: 0.6687 (mtt90) REVERT: A 90 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6845 (t70) REVERT: A 161 SER cc_start: 0.8485 (t) cc_final: 0.8277 (m) REVERT: A 214 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.5963 (mp10) REVERT: C 21 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7768 (m) REVERT: C 81 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5659 (tt) REVERT: C 295 MET cc_start: 0.7218 (mmt) cc_final: 0.6288 (mmt) outliers start: 57 outliers final: 43 residues processed: 153 average time/residue: 0.1016 time to fit residues: 20.9489 Evaluate side-chains 138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.214402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.180703 restraints weight = 11233.138| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.58 r_work: 0.4088 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8803 Z= 0.175 Angle : 0.677 6.760 12023 Z= 0.358 Chirality : 0.046 0.192 1368 Planarity : 0.005 0.068 1407 Dihedral : 19.219 89.556 1407 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 5.62 % Allowed : 29.78 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.37 (0.25), residues: 955 helix: -0.89 (0.31), residues: 269 sheet: -2.77 (0.33), residues: 211 loop : -2.80 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 26 TYR 0.021 0.002 TYR A 300 PHE 0.017 0.002 PHE B 63 TRP 0.018 0.002 TRP C 129 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 8803) covalent geometry : angle 0.67717 / 0.36 (12023) hydrogen bonds : bond 0.03783 / 2.33 ( 202) hydrogen bonds : angle 5.53497 / 4.18 ( 565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 101 time to evaluate : 0.347 Fit side-chains REVERT: F 41 ILE cc_start: 0.7544 (mt) cc_final: 0.7103 (tt) REVERT: B 35 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6632 (tpt170) REVERT: B 114 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8060 (tttm) REVERT: B 144 TYR cc_start: 0.6539 (m-10) cc_final: 0.6188 (m-10) REVERT: A 90 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6706 (t70) REVERT: A 161 SER cc_start: 0.8418 (t) cc_final: 0.8194 (m) REVERT: A 214 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6063 (mp10) REVERT: C 21 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7613 (m) REVERT: C 81 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5522 (tt) REVERT: C 295 MET cc_start: 0.7178 (mmt) cc_final: 0.6392 (mmt) outliers start: 50 outliers final: 44 residues processed: 145 average time/residue: 0.1023 time to fit residues: 20.3226 Evaluate side-chains 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.210233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178348 restraints weight = 11136.888| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.22 r_work: 0.4079 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8803 Z= 0.146 Angle : 0.649 7.114 12023 Z= 0.342 Chirality : 0.045 0.180 1368 Planarity : 0.004 0.048 1407 Dihedral : 19.121 89.316 1407 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 5.84 % Allowed : 30.22 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.21 (0.25), residues: 955 helix: -0.69 (0.32), residues: 267 sheet: -2.61 (0.34), residues: 206 loop : -2.78 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.018 0.002 TYR A 300 PHE 0.029 0.002 PHE A 156 TRP 0.019 0.001 TRP C 129 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 8803) covalent geometry : angle 0.64939 / 0.34 (12023) hydrogen bonds : bond 0.03431 / 2.13 ( 202) hydrogen bonds : angle 5.34334 / 4.03 ( 565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 0.306 Fit side-chains REVERT: F 41 ILE cc_start: 0.7416 (mt) cc_final: 0.6967 (tt) REVERT: B 35 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6632 (tpt170) REVERT: B 114 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8114 (tttm) REVERT: B 144 TYR cc_start: 0.6474 (m-10) cc_final: 0.6198 (m-10) REVERT: A 90 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6834 (t0) REVERT: A 161 SER cc_start: 0.8385 (t) cc_final: 0.8182 (m) REVERT: A 214 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6036 (mp10) REVERT: C 21 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7646 (m) REVERT: C 41 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7756 (m100) REVERT: C 173 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6196 (mp) REVERT: C 295 MET cc_start: 0.7112 (mmt) cc_final: 0.6352 (mmt) REVERT: C 333 CYS cc_start: 0.5507 (OUTLIER) cc_final: 0.4964 (p) outliers start: 52 outliers final: 39 residues processed: 146 average time/residue: 0.0956 time to fit residues: 19.2983 Evaluate side-chains 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.0010 chunk 77 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 ASN A 246 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.218245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.185185 restraints weight = 11138.522| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.48 r_work: 0.4141 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8803 Z= 0.120 Angle : 0.626 7.097 12023 Z= 0.329 Chirality : 0.044 0.198 1368 Planarity : 0.004 0.071 1407 Dihedral : 18.982 88.366 1404 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 5.17 % Allowed : 30.67 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -3.04 (0.26), residues: 955 helix: -0.49 (0.32), residues: 269 sheet: -2.57 (0.34), residues: 208 loop : -2.69 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 26 TYR 0.023 0.001 TYR A 10 PHE 0.025 0.001 PHE C 257 TRP 0.019 0.001 TRP C 129 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8803) covalent geometry : angle 0.62560 / 0.33 (12023) hydrogen bonds : bond 0.03123 / 1.94 ( 202) hydrogen bonds : angle 5.16942 / 3.89 ( 565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 0.312 Fit side-chains REVERT: F 41 ILE cc_start: 0.7268 (mt) cc_final: 0.6893 (tt) REVERT: B 35 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6555 (tpt170) REVERT: B 114 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8080 (tttm) REVERT: B 144 TYR cc_start: 0.6526 (m-10) cc_final: 0.6205 (m-10) REVERT: A 90 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6722 (t0) REVERT: A 161 SER cc_start: 0.8397 (t) cc_final: 0.8131 (m) REVERT: A 200 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.6342 (mt0) REVERT: A 214 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.5906 (mp10) REVERT: C 21 SER cc_start: 0.7849 (m) cc_final: 0.7586 (m) REVERT: C 41 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.7711 (m100) REVERT: C 173 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6127 (mp) REVERT: C 295 MET cc_start: 0.7099 (mmt) cc_final: 0.6332 (mmt) outliers start: 46 outliers final: 36 residues processed: 140 average time/residue: 0.0940 time to fit residues: 17.8141 Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.217529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.184966 restraints weight = 11165.775| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.68 r_work: 0.4116 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8803 Z= 0.135 Angle : 0.633 8.391 12023 Z= 0.332 Chirality : 0.044 0.165 1368 Planarity : 0.004 0.046 1407 Dihedral : 18.984 87.817 1402 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 5.51 % Allowed : 30.67 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.99 (0.26), residues: 955 helix: -0.38 (0.33), residues: 263 sheet: -2.54 (0.34), residues: 208 loop : -2.67 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.017 0.002 TYR A 300 PHE 0.016 0.001 PHE B 63 TRP 0.019 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8803) covalent geometry : angle 0.63273 / 0.33 (12023) hydrogen bonds : bond 0.03193 / 1.99 ( 202) hydrogen bonds : angle 5.13622 / 3.86 ( 565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 0.314 Fit side-chains REVERT: F 41 ILE cc_start: 0.7188 (mt) cc_final: 0.6781 (tt) REVERT: B 35 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6534 (tpt170) REVERT: B 114 LYS cc_start: 0.8365 (ttpp) cc_final: 0.8064 (tttm) REVERT: B 144 TYR cc_start: 0.6628 (m-10) cc_final: 0.6285 (m-10) REVERT: A 90 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6690 (t0) REVERT: A 161 SER cc_start: 0.8406 (t) cc_final: 0.8167 (m) REVERT: A 200 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6563 (mt0) REVERT: A 214 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6072 (mp10) REVERT: A 396 LYS cc_start: 0.4835 (OUTLIER) cc_final: 0.4546 (ttmt) REVERT: C 21 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7685 (m) REVERT: C 41 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.7663 (m100) REVERT: C 173 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6139 (mp) REVERT: C 295 MET cc_start: 0.7113 (mmt) cc_final: 0.6316 (mmt) outliers start: 49 outliers final: 38 residues processed: 134 average time/residue: 0.0912 time to fit residues: 16.9014 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 7.9990 chunk 37 optimal weight: 0.0970 chunk 8 optimal weight: 0.0170 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.0170 chunk 49 optimal weight: 0.0050 chunk 65 optimal weight: 1.9990 overall best weight: 0.1668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 ASN A 246 HIS A 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.215861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.185515 restraints weight = 10901.592| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.23 r_work: 0.4194 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8803 Z= 0.111 Angle : 0.614 7.847 12023 Z= 0.323 Chirality : 0.043 0.166 1368 Planarity : 0.004 0.076 1407 Dihedral : 18.888 87.032 1402 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.49 % Allowed : 31.57 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.78 (0.26), residues: 955 helix: -0.24 (0.33), residues: 268 sheet: -2.25 (0.35), residues: 207 loop : -2.64 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.017 0.001 TYR A 10 PHE 0.020 0.001 PHE C 257 TRP 0.021 0.001 TRP C 129 HIS 0.005 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 8803) covalent geometry : angle 0.61358 / 0.32 (12023) hydrogen bonds : bond 0.02862 / 1.78 ( 202) hydrogen bonds : angle 4.98449 / 3.73 ( 565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.213 Fit side-chains REVERT: F 41 ILE cc_start: 0.7008 (mt) cc_final: 0.6711 (tt) REVERT: B 35 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6457 (tpt170) REVERT: B 114 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7969 (tttm) REVERT: B 144 TYR cc_start: 0.6439 (m-10) cc_final: 0.6150 (m-10) REVERT: A 161 SER cc_start: 0.8280 (t) cc_final: 0.8025 (m) REVERT: A 200 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6418 (mt0) REVERT: A 214 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.5928 (mp10) REVERT: A 396 LYS cc_start: 0.4859 (OUTLIER) cc_final: 0.4575 (ttmt) REVERT: C 21 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.7525 (m) REVERT: C 173 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6200 (mp) REVERT: C 295 MET cc_start: 0.7062 (mmt) cc_final: 0.6315 (mmt) outliers start: 40 outliers final: 23 residues processed: 122 average time/residue: 0.0926 time to fit residues: 15.6023 Evaluate side-chains 116 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 0.0040 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.214123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.183078 restraints weight = 10871.587| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.26 r_work: 0.4180 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8803 Z= 0.128 Angle : 0.628 7.826 12023 Z= 0.327 Chirality : 0.043 0.160 1368 Planarity : 0.004 0.072 1407 Dihedral : 18.845 86.796 1394 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.93 % Allowed : 31.57 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % 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: -2.77 (0.26), residues: 955 helix: -0.16 (0.34), residues: 262 sheet: -2.33 (0.35), residues: 213 loop : -2.60 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.014 0.001 TYR A 300 PHE 0.021 0.001 PHE B 90 TRP 0.034 0.002 TRP C 41 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8803) covalent geometry : angle 0.62777 / 0.33 (12023) hydrogen bonds : bond 0.02969 / 1.85 ( 202) hydrogen bonds : angle 4.93049 / 3.68 ( 565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.22 seconds wall clock time: 32 minutes 17.00 seconds (1937.00 seconds total)