Starting phenix.real_space_refine on Fri Aug 22 23:17:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8urq_42497/08_2025/8urq_42497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urq_42497/08_2025/8urq_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 { model { file = "/net/cci-nas-00/data/ceres_data/8urq_42497/08_2025/8urq_42497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urq_42497/08_2025/8urq_42497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8urq_42497/08_2025/8urq_42497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urq_42497/08_2025/8urq_42497.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-2.0-5787/lib/python3.9/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: 2.30, per 1000 atoms: 0.27 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: 0.91 Conformation dependent library (CDL) restraints added in 229.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.03 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: 1.32 Time building geometry restraints manager: 1.20 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: 1274 0.103 - 0.206: 81 0.206 - 0.308: 12 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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= 1.205 Angle : 1.247 57.670 12023 Z= 0.810 Chirality : 0.057 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 aren 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 covalent geometry : bond 0.01707 ( 8803) covalent geometry : angle 1.24705 (12023) hydrogen bonds : bond 0.23323 ( 202) hydrogen bonds : angle 9.51120 ( 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 : 0.228 Fit side-chains REVERT: F 15 GLN cc_start: 0.6237 (OUTLIER) cc_final: 0.5572 (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: 0.8136 (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: 0.7708 (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: 0.1122 time to fit residues: 23.1335 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 : 0.197 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 86 HIS A 101 HIS A 144 GLN A 370 ASN ** 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 = 0.215397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.184798 restraints weight = 11059.484| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.44 r_work: 0.4195 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8803 Z= 0.138 Angle : 0.637 6.965 12023 Z= 0.341 Chirality : 0.044 0.219 1368 Planarity : 0.004 0.057 1407 Dihedral : 19.484 84.265 1457 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.05 % Favored : 89.84 % Rotamer: Outliers : 6.18 % Allowed : 28.65 % Favored : 65.17 % 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 aren not related in a simple way. whole: -3.47 (0.25), residues: 955 helix: -0.77 (0.32), residues: 257 sheet: -2.97 (0.33), residues: 212 loop : -2.88 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 245 TYR 0.017 0.001 TYR A 300 PHE 0.015 0.001 PHE C 257 TRP 0.013 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8803) covalent geometry : angle 0.63736 (12023) hydrogen bonds : bond 0.03675 ( 202) hydrogen bonds : angle 5.71375 ( 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 169 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7976 (mt) cc_final: 0.7309 (tt) REVERT: B 144 TYR cc_start: 0.6264 (m-80) cc_final: 0.5831 (m-10) REVERT: A 267 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6896 (tp) REVERT: C 21 SER cc_start: 0.7933 (m) cc_final: 0.7691 (m) REVERT: C 41 TRP cc_start: 0.7993 (OUTLIER) cc_final: 0.7779 (m100) REVERT: C 295 MET cc_start: 0.7005 (mmt) cc_final: 0.6077 (mmt) REVERT: C 343 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4813 (tt) outliers start: 55 outliers final: 29 residues processed: 162 average time/residue: 0.1052 time to fit residues: 22.9824 Evaluate side-chains 130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 34 VAL 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 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 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 41 TRP 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 224 GLU Chi-restraints excluded: chain C residue 297 LEU 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: 2.9990 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 0.0060 chunk 20 optimal weight: 0.2980 chunk 63 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS C 43 ASN C 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.216639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185700 restraints weight = 10877.302| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.42 r_work: 0.4208 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8803 Z= 0.117 Angle : 0.596 7.375 12023 Z= 0.314 Chirality : 0.042 0.180 1368 Planarity : 0.005 0.119 1407 Dihedral : 18.908 88.927 1408 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 5.51 % Allowed : 27.87 % Favored : 66.63 % 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 aren not related in a simple way. whole: -3.16 (0.25), residues: 955 helix: -0.55 (0.32), residues: 264 sheet: -2.64 (0.33), residues: 214 loop : -2.76 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 24 TYR 0.013 0.001 TYR A 300 PHE 0.015 0.001 PHE B 63 TRP 0.014 0.001 TRP C 129 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8803) covalent geometry : angle 0.59580 (12023) hydrogen bonds : bond 0.03243 ( 202) hydrogen bonds : angle 5.24978 ( 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 153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7664 (mt) cc_final: 0.7087 (tt) REVERT: B 35 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6851 (tpt170) REVERT: B 144 TYR cc_start: 0.6327 (m-10) cc_final: 0.5960 (m-10) REVERT: A 107 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6918 (ptm160) REVERT: A 200 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6355 (mt0) REVERT: A 299 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7176 (t0) REVERT: C 21 SER cc_start: 0.7910 (m) cc_final: 0.7670 (m) REVERT: C 295 MET cc_start: 0.6991 (mmt) cc_final: 0.6048 (mmt) outliers start: 49 outliers final: 30 residues processed: 147 average time/residue: 0.1057 time to fit residues: 21.3762 Evaluate side-chains 122 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 THR 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 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 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain C residue 40 VAL 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 301 ASP Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.0370 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.0030 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 overall best weight: 0.3306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 HIS A 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.223212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.191106 restraints weight = 11264.912| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 2.49 r_work: 0.4217 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8803 Z= 0.108 Angle : 0.593 12.871 12023 Z= 0.306 Chirality : 0.041 0.159 1368 Planarity : 0.004 0.063 1407 Dihedral : 18.806 89.809 1407 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.62 % Allowed : 27.64 % Favored : 66.74 % 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 aren not related in a simple way. whole: -2.83 (0.26), residues: 955 helix: -0.11 (0.34), residues: 256 sheet: -2.33 (0.34), residues: 215 loop : -2.69 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.015 0.001 TYR C 56 PHE 0.016 0.001 PHE C 257 TRP 0.015 0.001 TRP C 129 HIS 0.010 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8803) covalent geometry : angle 0.59303 (12023) hydrogen bonds : bond 0.02879 ( 202) hydrogen bonds : angle 4.98759 ( 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 152 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 40 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7344 (mtp85) REVERT: F 41 ILE cc_start: 0.7176 (mt) cc_final: 0.6823 (tt) REVERT: B 35 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6724 (tpt170) REVERT: B 74 GLN cc_start: 0.3339 (OUTLIER) cc_final: 0.2875 (pp30) REVERT: B 114 LYS cc_start: 0.8325 (ttpp) cc_final: 0.7930 (tttm) REVERT: B 144 TYR cc_start: 0.6240 (m-10) cc_final: 0.5889 (m-10) REVERT: A 161 SER cc_start: 0.8250 (t) cc_final: 0.7939 (m) REVERT: A 200 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6449 (mm-40) REVERT: A 299 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7207 (t0) REVERT: C 21 SER cc_start: 0.7870 (m) cc_final: 0.7647 (m) REVERT: C 81 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.5309 (tt) REVERT: C 178 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 295 MET cc_start: 0.6911 (mmt) cc_final: 0.5954 (mmt) REVERT: C 343 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4900 (tt) outliers start: 50 outliers final: 27 residues processed: 144 average time/residue: 0.1121 time to fit residues: 21.8215 Evaluate side-chains 125 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 74 GLN 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 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 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 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 359 ASN 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 178 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 221 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 80 optimal weight: 0.0370 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS C 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.214706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.181793 restraints weight = 10952.595| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.21 r_work: 0.4179 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8803 Z= 0.134 Angle : 0.611 10.692 12023 Z= 0.318 Chirality : 0.042 0.174 1368 Planarity : 0.004 0.055 1407 Dihedral : 18.822 89.407 1398 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.17 % Allowed : 28.99 % Favored : 65.84 % 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 aren not related in a simple way. whole: -2.89 (0.26), residues: 955 helix: -0.26 (0.33), residues: 263 sheet: -2.43 (0.33), residues: 226 loop : -2.64 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 245 TYR 0.018 0.001 TYR A 300 PHE 0.011 0.001 PHE C 155 TRP 0.015 0.001 TRP C 129 HIS 0.012 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8803) covalent geometry : angle 0.61094 (12023) hydrogen bonds : bond 0.03056 ( 202) hydrogen bonds : angle 5.02736 ( 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 146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7317 (mt) cc_final: 0.6928 (tt) REVERT: B 35 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6651 (tpt170) REVERT: B 114 LYS cc_start: 0.8350 (ttpp) cc_final: 0.7986 (tttm) REVERT: B 144 TYR cc_start: 0.6347 (m-10) cc_final: 0.5999 (m-10) REVERT: A 107 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6780 (ptm160) REVERT: A 214 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.5960 (mp10) REVERT: A 299 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7455 (t0) REVERT: C 21 SER cc_start: 0.7937 (m) cc_final: 0.7681 (m) REVERT: C 81 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5447 (tt) REVERT: C 178 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8520 (p) REVERT: C 295 MET cc_start: 0.6997 (mmt) cc_final: 0.6091 (mmt) REVERT: C 343 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5135 (tt) outliers start: 46 outliers final: 30 residues processed: 140 average time/residue: 0.1128 time to fit residues: 21.4445 Evaluate side-chains 125 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 102 VAL 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 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 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 214 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 375 CYS Chi-restraints excluded: chain A residue 386 GLU 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 178 THR 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 343 LEU Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.212899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.180945 restraints weight = 10987.209| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.30 r_work: 0.4144 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8803 Z= 0.151 Angle : 0.624 9.127 12023 Z= 0.327 Chirality : 0.043 0.160 1368 Planarity : 0.005 0.099 1407 Dihedral : 18.725 89.102 1395 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 5.73 % Allowed : 28.20 % Favored : 66.07 % 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 aren not related in a simple way. whole: -2.93 (0.26), residues: 955 helix: -0.40 (0.33), residues: 267 sheet: -2.44 (0.33), residues: 224 loop : -2.62 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.020 0.001 TYR A 300 PHE 0.015 0.001 PHE C 257 TRP 0.015 0.001 TRP C 129 HIS 0.017 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8803) covalent geometry : angle 0.62417 (12023) hydrogen bonds : bond 0.03103 ( 202) hydrogen bonds : angle 5.11918 ( 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 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7267 (mt) cc_final: 0.6887 (tt) REVERT: B 35 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6593 (tpt170) REVERT: B 114 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8030 (tttm) REVERT: B 144 TYR cc_start: 0.6395 (m-10) cc_final: 0.6081 (m-10) REVERT: A 90 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6661 (t0) REVERT: A 107 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6796 (ptm160) REVERT: A 161 SER cc_start: 0.8419 (t) cc_final: 0.8161 (m) REVERT: A 214 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.5966 (mp10) REVERT: A 396 LYS cc_start: 0.4731 (OUTLIER) cc_final: 0.4461 (ttmt) REVERT: C 21 SER cc_start: 0.7947 (m) cc_final: 0.7671 (m) REVERT: C 81 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5389 (tt) REVERT: C 295 MET cc_start: 0.7056 (mmt) cc_final: 0.6183 (mmt) REVERT: C 343 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5144 (tt) outliers start: 51 outliers final: 35 residues processed: 143 average time/residue: 0.1118 time to fit residues: 21.7424 Evaluate side-chains 132 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 102 VAL 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 216 SER 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 100 THR 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 214 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 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 LYS 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 301 ASP Chi-restraints excluded: chain C residue 343 LEU 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: 6.9990 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4645 r_free = 0.4645 target = 0.219003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.182797 restraints weight = 11338.738| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 2.45 r_work: 0.4134 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2812 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= 0.141 Angle : 0.618 8.326 12023 Z= 0.326 Chirality : 0.042 0.182 1368 Planarity : 0.005 0.107 1407 Dihedral : 18.616 88.037 1391 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.51 % Allowed : 28.54 % Favored : 65.96 % 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 aren not related in a simple way. whole: -2.86 (0.26), residues: 955 helix: -0.39 (0.33), residues: 268 sheet: -2.40 (0.34), residues: 209 loop : -2.57 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG F 26 TYR 0.018 0.001 TYR A 300 PHE 0.017 0.001 PHE F 17 TRP 0.017 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8803) covalent geometry : angle 0.61792 (12023) hydrogen bonds : bond 0.03010 ( 202) hydrogen bonds : angle 5.06139 ( 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 143 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7110 (mt) cc_final: 0.6710 (tt) REVERT: B 35 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6494 (tpt170) REVERT: B 114 LYS cc_start: 0.8293 (ttpp) cc_final: 0.7950 (tttm) REVERT: B 144 TYR cc_start: 0.6461 (m-10) cc_final: 0.6115 (m-10) REVERT: A 107 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6858 (ptm160) REVERT: A 161 SER cc_start: 0.8298 (t) cc_final: 0.7970 (m) REVERT: A 214 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.5953 (mp10) REVERT: A 396 LYS cc_start: 0.4776 (OUTLIER) cc_final: 0.4507 (ttmt) REVERT: C 21 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7705 (m) REVERT: C 41 TRP cc_start: 0.7963 (OUTLIER) cc_final: 0.7544 (m100) REVERT: C 56 TYR cc_start: 0.7283 (m-10) cc_final: 0.7016 (m-10) REVERT: C 81 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5556 (tt) REVERT: C 271 ILE cc_start: 0.7462 (mm) cc_final: 0.7131 (mt) REVERT: C 295 MET cc_start: 0.7077 (mmt) cc_final: 0.6212 (mmt) REVERT: C 343 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.4878 (tt) outliers start: 49 outliers final: 34 residues processed: 136 average time/residue: 0.0929 time to fit residues: 17.3777 Evaluate side-chains 131 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 89 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 102 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 151 THR 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 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 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS 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 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 301 ASP Chi-restraints excluded: chain C residue 343 LEU 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: 0.8980 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4647 r_free = 0.4647 target = 0.219201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.183322 restraints weight = 11133.562| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.41 r_work: 0.4139 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8803 Z= 0.134 Angle : 0.615 7.324 12023 Z= 0.323 Chirality : 0.042 0.187 1368 Planarity : 0.005 0.069 1407 Dihedral : 18.584 88.067 1391 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 5.17 % Allowed : 28.99 % Favored : 65.84 % 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 aren not related in a simple way. whole: -2.83 (0.26), residues: 955 helix: -0.42 (0.33), residues: 271 sheet: -2.38 (0.34), residues: 209 loop : -2.53 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.017 0.001 TYR A 300 PHE 0.037 0.001 PHE A 156 TRP 0.016 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8803) covalent geometry : angle 0.61537 (12023) hydrogen bonds : bond 0.02923 ( 202) hydrogen bonds : angle 4.99229 ( 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 143 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7087 (mt) cc_final: 0.6673 (tt) REVERT: B 35 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6489 (tpt170) REVERT: B 144 TYR cc_start: 0.6568 (m-10) cc_final: 0.6241 (m-10) REVERT: A 107 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6880 (ptm160) REVERT: A 161 SER cc_start: 0.8277 (t) cc_final: 0.7973 (m) REVERT: A 214 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.5945 (mp10) REVERT: A 396 LYS cc_start: 0.4881 (OUTLIER) cc_final: 0.4625 (ttmt) REVERT: C 21 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7692 (m) REVERT: C 41 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.7696 (m100) REVERT: C 81 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5500 (tt) REVERT: C 295 MET cc_start: 0.7080 (mmt) cc_final: 0.6250 (mmt) REVERT: C 343 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.5011 (tt) outliers start: 46 outliers final: 33 residues processed: 136 average time/residue: 0.0926 time to fit residues: 17.1678 Evaluate side-chains 132 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 102 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 185 GLU 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 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS 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 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 301 ASP Chi-restraints excluded: chain C residue 343 LEU 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: 1.9990 chunk 60 optimal weight: 0.1980 chunk 30 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4657 r_free = 0.4657 target = 0.220208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.184447 restraints weight = 11123.970| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.44 r_work: 0.4153 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8803 Z= 0.125 Angle : 0.611 8.030 12023 Z= 0.320 Chirality : 0.042 0.194 1368 Planarity : 0.005 0.068 1407 Dihedral : 18.539 87.583 1391 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.94 % Allowed : 29.10 % Favored : 65.96 % 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 aren not related in a simple way. whole: -2.77 (0.26), residues: 955 helix: -0.32 (0.33), residues: 270 sheet: -2.25 (0.33), residues: 216 loop : -2.56 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 26 TYR 0.016 0.001 TYR A 300 PHE 0.029 0.001 PHE A 156 TRP 0.017 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8803) covalent geometry : angle 0.61067 (12023) hydrogen bonds : bond 0.02808 ( 202) hydrogen bonds : angle 4.87842 ( 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 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.6831 (mt) cc_final: 0.6440 (tt) REVERT: B 35 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6419 (tpt170) REVERT: B 114 LYS cc_start: 0.8276 (tttm) cc_final: 0.7814 (tttm) REVERT: B 144 TYR cc_start: 0.6584 (m-10) cc_final: 0.6297 (m-10) REVERT: A 107 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6855 (ptm160) REVERT: A 161 SER cc_start: 0.8244 (t) cc_final: 0.7940 (m) REVERT: A 214 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.5954 (mp10) REVERT: A 396 LYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4755 (ttmt) REVERT: C 21 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7680 (m) REVERT: C 41 TRP cc_start: 0.7940 (OUTLIER) cc_final: 0.7513 (m100) REVERT: C 56 TYR cc_start: 0.7209 (m-10) cc_final: 0.6974 (m-10) REVERT: C 81 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5451 (tt) REVERT: C 271 ILE cc_start: 0.7448 (mm) cc_final: 0.7132 (mt) REVERT: C 295 MET cc_start: 0.7072 (mmt) cc_final: 0.6209 (mmt) REVERT: C 343 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4724 (tt) outliers start: 44 outliers final: 33 residues processed: 128 average time/residue: 0.1063 time to fit residues: 18.4814 Evaluate side-chains 127 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 GLU 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 46 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 107 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS 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 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 301 ASP Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN C 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.215802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.181177 restraints weight = 11136.054| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.27 r_work: 0.4117 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8803 Z= 0.180 Angle : 0.672 9.357 12023 Z= 0.352 Chirality : 0.044 0.196 1368 Planarity : 0.005 0.064 1407 Dihedral : 18.629 87.684 1391 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 4.72 % Allowed : 29.44 % Favored : 65.84 % 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 aren not related in a simple way. whole: -2.92 (0.26), residues: 955 helix: -0.52 (0.32), residues: 265 sheet: -2.45 (0.33), residues: 209 loop : -2.54 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 26 TYR 0.023 0.002 TYR A 300 PHE 0.026 0.002 PHE A 156 TRP 0.016 0.001 TRP C 129 HIS 0.008 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8803) covalent geometry : angle 0.67229 (12023) hydrogen bonds : bond 0.03312 ( 202) hydrogen bonds : angle 5.14217 ( 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 137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7008 (mt) cc_final: 0.6607 (tt) REVERT: B 144 TYR cc_start: 0.6706 (m-10) cc_final: 0.6414 (m-10) REVERT: A 90 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6723 (t0) REVERT: A 107 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6886 (ptm160) REVERT: A 161 SER cc_start: 0.8416 (t) cc_final: 0.8138 (m) REVERT: A 214 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.5982 (mp10) REVERT: A 396 LYS cc_start: 0.5048 (OUTLIER) cc_final: 0.4784 (ttmt) REVERT: C 21 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7686 (m) REVERT: C 41 TRP cc_start: 0.7970 (OUTLIER) cc_final: 0.7581 (m100) REVERT: C 56 TYR cc_start: 0.7528 (m-10) cc_final: 0.7321 (m-10) REVERT: C 295 MET cc_start: 0.7161 (mmt) cc_final: 0.6253 (mmt) outliers start: 42 outliers final: 31 residues processed: 130 average time/residue: 0.1071 time to fit residues: 18.8304 Evaluate side-chains 128 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS 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 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 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 10 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4649 r_free = 0.4649 target = 0.219274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.185377 restraints weight = 11039.478| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.25 r_work: 0.4168 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8803 Z= 0.128 Angle : 0.637 8.743 12023 Z= 0.334 Chirality : 0.042 0.194 1368 Planarity : 0.004 0.056 1407 Dihedral : 18.505 87.725 1391 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.38 % Allowed : 29.78 % Favored : 65.84 % 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 aren not related in a simple way. whole: -2.73 (0.26), residues: 955 helix: -0.27 (0.34), residues: 262 sheet: -2.27 (0.33), residues: 217 loop : -2.49 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 25 TYR 0.015 0.001 TYR A 300 PHE 0.027 0.001 PHE A 156 TRP 0.018 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8803) covalent geometry : angle 0.63717 (12023) hydrogen bonds : bond 0.02852 ( 202) hydrogen bonds : angle 4.90028 ( 565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.37 seconds wall clock time: 36 minutes 26.34 seconds (2186.34 seconds total)