Starting phenix.real_space_refine on Wed Jan 15 14:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8urq_42497/01_2025/8urq_42497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urq_42497/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8urq_42497/01_2025/8urq_42497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urq_42497/01_2025/8urq_42497.map" model { file = "/net/cci-nas-00/data/ceres_data/8urq_42497/01_2025/8urq_42497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urq_42497/01_2025/8urq_42497.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'PHE:plan': 1, 'ASN:plan1': 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: 5.12, per 1000 atoms: 0.60 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: 2.23 Conformation dependent library (CDL) restraints added in 886.5 milliseconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 26.7% alpha, 12.1% beta 5 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.65 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: 2.18 Time building geometry restraints manager: 2.53 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: 0.750 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.050 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- 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= 1.291 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (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 TRP 0.017 0.002 TRP C 129 HIS 0.004 0.001 HIS A 63 PHE 0.026 0.002 PHE C 288 TYR 0.031 0.002 TYR C 56 ARG 0.005 0.000 ARG A 163 *********************** 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 : 0.856 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: 0.2532 time to fit residues: 52.0796 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 : 0.864 ------------------------------------------------------------------------------- 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 84 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 102 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.221872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.189621 restraints weight = 11047.342| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.40 r_work: 0.4212 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1602 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= 0.179 Angle : 0.624 6.680 12023 Z= 0.334 Chirality : 0.043 0.204 1368 Planarity : 0.004 0.058 1407 Dihedral : 19.447 85.056 1457 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.53 % Favored : 90.37 % Rotamer: Outliers : 6.07 % Allowed : 28.54 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.25), residues: 955 helix: -0.74 (0.32), residues: 257 sheet: -2.96 (0.33), residues: 212 loop : -2.86 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 PHE 0.014 0.001 PHE C 257 TYR 0.015 0.001 TYR A 300 ARG 0.006 0.001 ARG B 245 *********************** 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 168 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7954 (mt) cc_final: 0.7293 (tt) REVERT: B 144 TYR cc_start: 0.6250 (m-80) cc_final: 0.5841 (m-10) REVERT: A 267 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6942 (tp) REVERT: C 21 SER cc_start: 0.7908 (m) cc_final: 0.7690 (m) REVERT: C 41 TRP cc_start: 0.7959 (OUTLIER) cc_final: 0.7748 (m100) REVERT: C 295 MET cc_start: 0.6982 (mmt) cc_final: 0.6026 (mmt) REVERT: C 343 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4744 (tt) outliers start: 54 outliers final: 29 residues processed: 161 average time/residue: 0.2279 time to fit residues: 49.6183 Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.4980 chunk 40 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.214851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.183713 restraints weight = 11013.946| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 2.37 r_work: 0.4181 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1987 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= 0.184 Angle : 0.604 7.067 12023 Z= 0.321 Chirality : 0.042 0.183 1368 Planarity : 0.004 0.044 1407 Dihedral : 18.948 89.069 1408 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 5.51 % Allowed : 27.98 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.25), residues: 955 helix: -0.55 (0.32), residues: 265 sheet: -2.75 (0.32), residues: 221 loop : -2.76 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 129 HIS 0.006 0.001 HIS C 156 PHE 0.016 0.001 PHE B 63 TYR 0.016 0.001 TYR A 300 ARG 0.004 0.000 ARG A 163 *********************** 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 155 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 106 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7727 (mt) cc_final: 0.7119 (tt) REVERT: B 35 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6911 (tpt170) REVERT: B 144 TYR cc_start: 0.6205 (m-10) cc_final: 0.5870 (m-10) REVERT: A 107 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6908 (ptm160) REVERT: A 200 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6383 (mt0) REVERT: A 267 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7084 (tp) REVERT: A 299 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7195 (t0) REVERT: C 21 SER cc_start: 0.7944 (m) cc_final: 0.7718 (m) REVERT: C 295 MET cc_start: 0.6983 (mmt) cc_final: 0.6029 (mmt) outliers start: 49 outliers final: 31 residues processed: 147 average time/residue: 0.2356 time to fit residues: 46.5939 Evaluate side-chains 129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain B residue 102 VAL 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 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 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 195 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 250 ILE 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 25 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.0050 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 HIS A 102 GLN A 246 HIS C 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.218295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.184053 restraints weight = 11280.268| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.59 r_work: 0.4138 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8803 Z= 0.218 Angle : 0.614 6.533 12023 Z= 0.326 Chirality : 0.043 0.159 1368 Planarity : 0.004 0.042 1407 Dihedral : 18.970 89.915 1406 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 6.07 % Allowed : 28.99 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.26), residues: 955 helix: -0.42 (0.33), residues: 263 sheet: -2.57 (0.33), residues: 222 loop : -2.68 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 129 HIS 0.012 0.001 HIS C 156 PHE 0.015 0.001 PHE C 257 TYR 0.019 0.001 TYR A 300 ARG 0.005 0.000 ARG A 163 *********************** 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 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7389 (mt) cc_final: 0.6949 (tt) REVERT: B 35 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6649 (tpt170) REVERT: B 114 LYS cc_start: 0.8324 (ttpp) cc_final: 0.7963 (tttm) REVERT: B 144 TYR cc_start: 0.6182 (m-10) cc_final: 0.5842 (m-10) REVERT: A 90 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6668 (t0) REVERT: A 107 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6969 (ptm160) REVERT: A 161 SER cc_start: 0.8348 (t) cc_final: 0.8053 (m) REVERT: A 200 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6455 (mt0) REVERT: A 214 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.5983 (mp10) REVERT: A 267 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7096 (tp) REVERT: A 299 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7501 (t0) REVERT: C 21 SER cc_start: 0.7988 (m) cc_final: 0.7736 (m) REVERT: C 41 TRP cc_start: 0.7970 (OUTLIER) cc_final: 0.7746 (m100) REVERT: C 81 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5510 (tt) REVERT: C 295 MET cc_start: 0.7071 (mmt) cc_final: 0.6161 (mmt) REVERT: C 343 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5113 (tt) outliers start: 54 outliers final: 32 residues processed: 149 average time/residue: 0.2323 time to fit residues: 46.4698 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 : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN 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 313 MET 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 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 221 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 98 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- 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 = 0.4606 r_free = 0.4606 target = 0.213005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.181902 restraints weight = 10977.256| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.19 r_work: 0.4115 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8803 Z= 0.203 Angle : 0.628 15.425 12023 Z= 0.327 Chirality : 0.043 0.181 1368 Planarity : 0.005 0.117 1407 Dihedral : 18.866 89.130 1406 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 5.39 % Allowed : 28.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.26), residues: 955 helix: -0.34 (0.33), residues: 264 sheet: -2.55 (0.33), residues: 224 loop : -2.65 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 129 HIS 0.006 0.001 HIS C 66 PHE 0.012 0.001 PHE B 63 TYR 0.018 0.001 TYR A 300 ARG 0.021 0.001 ARG F 26 *********************** 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 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7314 (mt) cc_final: 0.6961 (tt) REVERT: B 35 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6619 (tpt170) REVERT: B 144 TYR cc_start: 0.6151 (m-10) cc_final: 0.5898 (m-10) REVERT: A 161 SER cc_start: 0.8374 (t) cc_final: 0.8120 (m) REVERT: A 200 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6477 (mt0) REVERT: A 214 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6111 (mp10) REVERT: A 267 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7191 (tp) REVERT: A 299 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7622 (t0) REVERT: C 21 SER cc_start: 0.7939 (m) cc_final: 0.7682 (m) REVERT: C 41 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.7810 (m100) REVERT: C 81 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5441 (tt) REVERT: C 295 MET cc_start: 0.7013 (mmt) cc_final: 0.6151 (mmt) REVERT: C 343 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.5192 (tt) outliers start: 48 outliers final: 35 residues processed: 143 average time/residue: 0.2248 time to fit residues: 44.2586 Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 106 LYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 359 ASN 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 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 221 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS A 323 GLN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.204056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.169935 restraints weight = 11051.010| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.37 r_work: 0.4034 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8803 Z= 0.457 Angle : 0.782 13.824 12023 Z= 0.415 Chirality : 0.048 0.156 1368 Planarity : 0.005 0.049 1407 Dihedral : 19.128 87.460 1400 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 6.85 % Allowed : 28.65 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.25), residues: 955 helix: -1.09 (0.31), residues: 266 sheet: -2.86 (0.33), residues: 206 loop : -2.78 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 129 HIS 0.014 0.002 HIS C 66 PHE 0.022 0.002 PHE B 176 TYR 0.032 0.003 TYR A 300 ARG 0.017 0.001 ARG F 26 *********************** 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 160 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 99 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: F 17 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6383 (t80) REVERT: B 144 TYR cc_start: 0.6579 (m-10) cc_final: 0.6253 (m-10) REVERT: A 107 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7061 (ptm160) REVERT: A 214 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6012 (mp10) REVERT: A 267 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7416 (tp) REVERT: A 396 LYS cc_start: 0.5134 (OUTLIER) cc_final: 0.4870 (ttmt) REVERT: C 21 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7785 (m) REVERT: C 41 TRP cc_start: 0.8128 (OUTLIER) cc_final: 0.7771 (m100) REVERT: C 81 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5756 (tt) REVERT: C 173 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5768 (mp) REVERT: C 295 MET cc_start: 0.7258 (mmt) cc_final: 0.6380 (mmt) REVERT: C 333 CYS cc_start: 0.5688 (OUTLIER) cc_final: 0.5161 (p) outliers start: 61 outliers final: 38 residues processed: 151 average time/residue: 0.2383 time to fit residues: 48.3656 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 87 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 110 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 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 173 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 39 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 ** C 72 GLN ** 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 = 0.4581 r_free = 0.4581 target = 0.210269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.177721 restraints weight = 11104.842| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.30 r_work: 0.4129 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3073 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= 0.197 Angle : 0.630 12.043 12023 Z= 0.332 Chirality : 0.042 0.160 1368 Planarity : 0.004 0.044 1407 Dihedral : 18.828 88.892 1400 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 5.62 % Allowed : 29.55 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.26), residues: 955 helix: -0.63 (0.33), residues: 263 sheet: -2.74 (0.32), residues: 224 loop : -2.65 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 129 HIS 0.007 0.001 HIS C 66 PHE 0.032 0.001 PHE A 156 TYR 0.019 0.002 TYR C 56 ARG 0.005 0.000 ARG F 40 *********************** 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 158 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: F 10 LYS cc_start: 0.6059 (ptmt) cc_final: 0.5688 (pttm) REVERT: F 41 ILE cc_start: 0.7318 (mt) cc_final: 0.6843 (tt) REVERT: B 35 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6362 (tpt170) REVERT: B 114 LYS cc_start: 0.8377 (tttm) cc_final: 0.7977 (tttm) REVERT: B 144 TYR cc_start: 0.6434 (m-80) cc_final: 0.6182 (m-10) REVERT: A 102 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7394 (tp40) REVERT: A 107 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6955 (ptm160) REVERT: A 214 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.5930 (mp10) REVERT: C 21 SER cc_start: 0.7904 (OUTLIER) cc_final: 0.7625 (m) REVERT: C 41 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7782 (m100) REVERT: C 81 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5557 (tt) REVERT: C 295 MET cc_start: 0.7133 (mmt) cc_final: 0.6422 (mmt) outliers start: 50 outliers final: 32 residues processed: 152 average time/residue: 0.2345 time to fit residues: 48.0753 Evaluate side-chains 133 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 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 381 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 41 optimal weight: 0.0040 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN A 246 HIS A 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.219705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.183912 restraints weight = 11280.627| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.46 r_work: 0.4150 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8803 Z= 0.167 Angle : 0.626 10.138 12023 Z= 0.327 Chirality : 0.042 0.181 1368 Planarity : 0.004 0.043 1407 Dihedral : 18.703 89.827 1398 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 5.28 % Allowed : 29.66 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.26), residues: 955 helix: -0.30 (0.34), residues: 260 sheet: -2.60 (0.32), residues: 223 loop : -2.59 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 129 HIS 0.004 0.001 HIS C 66 PHE 0.026 0.001 PHE C 257 TYR 0.015 0.001 TYR A 275 ARG 0.005 0.000 ARG F 40 *********************** 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 147 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: F 10 LYS cc_start: 0.6009 (ptmt) cc_final: 0.5633 (pttm) REVERT: F 26 ARG cc_start: 0.5454 (ptt-90) cc_final: 0.5243 (ptt-90) REVERT: F 41 ILE cc_start: 0.6996 (mt) cc_final: 0.6598 (tt) REVERT: B 35 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6332 (tpt170) REVERT: B 114 LYS cc_start: 0.8285 (tttm) cc_final: 0.7918 (tttm) REVERT: B 144 TYR cc_start: 0.6459 (m-80) cc_final: 0.6220 (m-10) REVERT: A 102 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7343 (tp40) REVERT: A 200 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6481 (mt0) REVERT: A 214 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.5940 (mp10) REVERT: A 396 LYS cc_start: 0.5040 (OUTLIER) cc_final: 0.4800 (ttmt) REVERT: C 21 SER cc_start: 0.7911 (m) cc_final: 0.7644 (m) REVERT: C 41 TRP cc_start: 0.8054 (OUTLIER) cc_final: 0.7837 (m100) outliers start: 47 outliers final: 29 residues processed: 141 average time/residue: 0.2359 time to fit residues: 44.8293 Evaluate side-chains 129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ILE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER 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 102 GLN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET 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 41 TRP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 173 LEU 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 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 12 optimal weight: 0.0010 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5506 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.213999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.181463 restraints weight = 11046.066| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.20 r_work: 0.4174 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8803 Z= 0.180 Angle : 0.631 9.778 12023 Z= 0.330 Chirality : 0.042 0.203 1368 Planarity : 0.004 0.043 1407 Dihedral : 18.611 88.733 1394 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.61 % Allowed : 30.00 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.26), residues: 955 helix: -0.22 (0.34), residues: 261 sheet: -2.56 (0.33), residues: 222 loop : -2.54 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 PHE 0.028 0.002 PHE C 288 TYR 0.015 0.001 TYR A 275 ARG 0.005 0.000 ARG A 163 *********************** 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 133 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: F 10 LYS cc_start: 0.5936 (ptmt) cc_final: 0.5501 (pttp) REVERT: F 41 ILE cc_start: 0.6890 (mt) cc_final: 0.6478 (tt) REVERT: B 35 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6363 (tpt170) REVERT: B 114 LYS cc_start: 0.8266 (tttm) cc_final: 0.7904 (tttm) REVERT: B 144 TYR cc_start: 0.6423 (m-80) cc_final: 0.6158 (m-10) REVERT: A 102 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7447 (tp40) REVERT: A 200 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6418 (mm-40) REVERT: A 214 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6055 (mp10) REVERT: A 396 LYS cc_start: 0.5089 (OUTLIER) cc_final: 0.4858 (ttmt) REVERT: C 21 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7677 (m) REVERT: C 41 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.7655 (m100) outliers start: 41 outliers final: 29 residues processed: 127 average time/residue: 0.2321 time to fit residues: 40.7244 Evaluate side-chains 127 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 102 GLN Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 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 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 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 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 C 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.219479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.184027 restraints weight = 11131.664| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.41 r_work: 0.4146 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3320 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= 0.189 Angle : 0.627 9.319 12023 Z= 0.328 Chirality : 0.042 0.194 1368 Planarity : 0.004 0.043 1407 Dihedral : 18.568 88.279 1394 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 4.83 % Allowed : 29.55 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.26), residues: 955 helix: -0.21 (0.34), residues: 261 sheet: -2.43 (0.33), residues: 219 loop : -2.52 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 PHE 0.025 0.002 PHE C 288 TYR 0.015 0.001 TYR A 300 ARG 0.006 0.000 ARG B 245 ********************** 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 131 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 88 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.6797 (mt) cc_final: 0.6378 (tt) REVERT: B 35 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6345 (tpt170) REVERT: B 114 LYS cc_start: 0.8261 (tttm) cc_final: 0.7894 (tttm) REVERT: B 144 TYR cc_start: 0.6547 (m-80) cc_final: 0.6272 (m-10) REVERT: A 102 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7496 (tp40) REVERT: A 214 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6078 (mp10) REVERT: A 396 LYS cc_start: 0.5139 (OUTLIER) cc_final: 0.4908 (ttmt) REVERT: C 21 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7702 (m) REVERT: C 41 TRP cc_start: 0.7982 (OUTLIER) cc_final: 0.7686 (m100) REVERT: C 295 MET cc_start: 0.7252 (mmt) cc_final: 0.6838 (mmt) outliers start: 43 outliers final: 29 residues processed: 124 average time/residue: 0.2239 time to fit residues: 38.0609 Evaluate side-chains 127 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 220 LEU 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 102 GLN 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 279 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 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 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 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 13 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN A 246 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.217288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.181284 restraints weight = 11296.629| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.43 r_work: 0.4115 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8803 Z= 0.229 Angle : 0.649 10.175 12023 Z= 0.341 Chirality : 0.043 0.191 1368 Planarity : 0.004 0.043 1407 Dihedral : 18.533 88.173 1391 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.16 % Allowed : 30.22 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.26), residues: 955 helix: -0.38 (0.33), residues: 264 sheet: -2.56 (0.32), residues: 224 loop : -2.49 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 129 HIS 0.008 0.001 HIS C 156 PHE 0.025 0.002 PHE C 288 TYR 0.019 0.001 TYR A 300 ARG 0.006 0.001 ARG B 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3894.20 seconds wall clock time: 70 minutes 11.02 seconds (4211.02 seconds total)