Starting phenix.real_space_refine on Thu Mar 13 02:14:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8urq_42497/03_2025/8urq_42497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urq_42497/03_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_42497/03_2025/8urq_42497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urq_42497/03_2025/8urq_42497.map" model { file = "/net/cci-nas-00/data/ceres_data/8urq_42497/03_2025/8urq_42497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urq_42497/03_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-5624/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: 5.67, per 1000 atoms: 0.66 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.63 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: 2.39 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.52: 5914 1.52 - 1.85: 2888 1.85 - 2.18: 0 2.18 - 2.52: 0 2.52 - 2.85: 1 Bond restraints: 8803 Sorted by residual: bond pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 1.329 2.851 -1.522 1.40e-02 5.10e+03 1.18e+04 bond pdb=" CA PRO A 96 " pdb=" C PRO A 96 " ideal model delta sigma weight residual 1.526 1.479 0.047 9.80e-03 1.04e+04 2.27e+01 bond pdb=" N ASP C 18 " pdb=" CA ASP C 18 " ideal model delta sigma weight residual 1.457 1.516 -0.058 1.29e-02 6.01e+03 2.04e+01 bond pdb=" C GLY A 257 " pdb=" O GLY A 257 " ideal model delta sigma weight residual 1.232 1.188 0.044 1.03e-02 9.43e+03 1.85e+01 bond pdb=" C TYR A 292 " pdb=" O TYR A 292 " ideal model delta sigma weight residual 1.237 1.183 0.054 1.36e-02 5.41e+03 1.55e+01 ... (remaining 8798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.53: 12018 11.53 - 23.07: 2 23.07 - 34.60: 0 34.60 - 46.14: 1 46.14 - 57.67: 2 Bond angle restraints: 12023 Sorted by residual: angle pdb=" O LEU B 12 " pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 122.20 64.53 57.67 1.34e+00 5.57e-01 1.85e+03 angle pdb=" CA LEU B 12 " pdb=" C LEU B 12 " pdb=" N SER B 28 " ideal model delta sigma weight residual 117.06 169.95 -52.89 1.53e+00 4.27e-01 1.20e+03 angle pdb=" C LEU B 12 " pdb=" N SER B 28 " pdb=" CA SER B 28 " ideal model delta sigma weight residual 121.70 85.35 36.35 1.80e+00 3.09e-01 4.08e+02 angle pdb=" N ILE A 353 " pdb=" CA ILE A 353 " pdb=" C ILE A 353 " ideal model delta sigma weight residual 111.90 101.91 9.99 8.10e-01 1.52e+00 1.52e+02 angle pdb=" N LYS A 258 " pdb=" CA LYS A 258 " pdb=" C LYS A 258 " ideal model delta sigma weight residual 111.28 123.48 -12.20 1.09e+00 8.42e-01 1.25e+02 ... (remaining 12018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4120 17.38 - 34.75: 666 34.75 - 52.13: 308 52.13 - 69.50: 82 69.50 - 86.88: 18 Dihedral angle restraints: 5194 sinusoidal: 2287 harmonic: 2907 Sorted by residual: dihedral pdb=" CA MET A 253 " pdb=" C MET A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PRO B 247 " pdb=" C PRO B 247 " pdb=" N PRO B 248 " pdb=" CA PRO B 248 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C LYS A 258 " pdb=" N LYS A 258 " pdb=" CA LYS A 258 " pdb=" CB LYS A 258 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 5191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1274 0.103 - 0.206: 81 0.206 - 0.308: 12 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA LYS A 258 " pdb=" N LYS A 258 " pdb=" C LYS A 258 " pdb=" CB LYS A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA PHE F 22 " pdb=" N PHE F 22 " pdb=" C PHE F 22 " pdb=" CB PHE F 22 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLN A 343 " pdb=" N GLN A 343 " pdb=" C GLN A 343 " pdb=" CB GLN A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1365 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 12 " 0.052 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C LEU B 12 " -0.086 2.00e-02 2.50e+03 pdb=" O LEU B 12 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 28 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC D 41 " -0.049 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" N1 DC D 41 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC D 41 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DC D 41 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC D 41 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC D 41 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC D 41 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC D 41 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC D 41 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 169 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A 170 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.047 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 33 2.40 - 3.02: 4835 3.02 - 3.65: 12661 3.65 - 4.27: 18672 4.27 - 4.90: 31171 Nonbonded interactions: 67372 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb="MG MG A 501 " model vdw 1.769 2.170 nonbonded pdb=" OD2 ASP A 290 " pdb="MG MG A 501 " model vdw 1.915 2.170 nonbonded pdb=" O HIS A 97 " pdb=" ND1 HIS A 97 " model vdw 2.129 3.120 nonbonded pdb=" O GLU A 235 " pdb=" OG1 THR A 239 " model vdw 2.225 3.040 nonbonded pdb=" O THR B 9 " pdb=" OG1 THR B 9 " model vdw 2.229 3.040 ... (remaining 67367 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.090 Process input model: 24.690 Find NCS groups from input model: 0.120 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- 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 : 0.918 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: 0.2577 time to fit residues: 53.3830 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 : 0.904 ------------------------------------------------------------------------------- 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: 0.3980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4681 r_free = 0.4681 target = 0.222597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.189673 restraints weight = 11057.458| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.47 r_work: 0.4196 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8803 Z= 0.175 Angle : 0.625 6.529 12023 Z= 0.334 Chirality : 0.043 0.201 1368 Planarity : 0.004 0.056 1407 Dihedral : 19.489 84.698 1457 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 6.07 % Allowed : 28.09 % 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: -3.43 (0.25), residues: 955 helix: -0.73 (0.32), residues: 257 sheet: -2.92 (0.32), residues: 214 loop : -2.87 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 129 HIS 0.005 0.001 HIS C 66 PHE 0.015 0.001 PHE C 257 TYR 0.015 0.001 TYR A 300 ARG 0.006 0.000 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 167 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7953 (mt) cc_final: 0.7321 (tt) REVERT: B 144 TYR cc_start: 0.6262 (m-10) cc_final: 0.5862 (m-10) REVERT: A 267 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6953 (tp) REVERT: C 21 SER cc_start: 0.7920 (m) cc_final: 0.7700 (m) REVERT: C 295 MET cc_start: 0.6968 (mmt) cc_final: 0.6002 (mmt) REVERT: C 343 LEU cc_start: 0.5226 (OUTLIER) cc_final: 0.4764 (tt) outliers start: 54 outliers final: 28 residues processed: 160 average time/residue: 0.2290 time to fit residues: 49.6785 Evaluate side-chains 129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 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: 0.0050 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS C 43 ASN C 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.213426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.181873 restraints weight = 11030.277| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.34 r_work: 0.4163 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8803 Z= 0.206 Angle : 0.627 8.773 12023 Z= 0.332 Chirality : 0.043 0.183 1368 Planarity : 0.004 0.046 1407 Dihedral : 19.000 88.597 1408 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 5.62 % Allowed : 28.31 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.24 (0.25), residues: 955 helix: -0.63 (0.32), residues: 266 sheet: -2.78 (0.32), residues: 221 loop : -2.74 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 129 HIS 0.007 0.001 HIS C 66 PHE 0.016 0.001 PHE B 63 TYR 0.019 0.002 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 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: F 41 ILE cc_start: 0.7758 (mt) cc_final: 0.7133 (tt) REVERT: B 35 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6833 (tpt170) REVERT: B 144 TYR cc_start: 0.6279 (m-10) cc_final: 0.5945 (m-10) REVERT: A 90 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6662 (t0) REVERT: A 161 SER cc_start: 0.8140 (t) cc_final: 0.7832 (m) REVERT: A 267 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7114 (tp) REVERT: A 299 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7366 (t0) REVERT: C 21 SER cc_start: 0.7969 (m) cc_final: 0.7733 (m) REVERT: C 81 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5453 (tt) REVERT: C 295 MET cc_start: 0.7008 (mmt) cc_final: 0.6057 (mmt) outliers start: 50 outliers final: 34 residues processed: 148 average time/residue: 0.2326 time to fit residues: 46.4435 Evaluate side-chains 130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain 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 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 A residue 340 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 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: 1.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.1624 ------------------------------------------------------------------------------- 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 48 ASN C 156 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.216959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.181824 restraints weight = 11303.053| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.82 r_work: 0.4097 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8803 Z= 0.243 Angle : 0.633 6.127 12023 Z= 0.336 Chirality : 0.043 0.162 1368 Planarity : 0.004 0.046 1407 Dihedral : 18.994 89.682 1407 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 6.40 % Allowed : 28.43 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.13 (0.25), residues: 955 helix: -0.60 (0.32), residues: 265 sheet: -2.57 (0.34), residues: 209 loop : -2.73 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 129 HIS 0.009 0.001 HIS C 156 PHE 0.016 0.001 PHE B 63 TYR 0.021 0.002 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 167 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 110 time to evaluate : 0.964 Fit side-chains REVERT: F 41 ILE cc_start: 0.7413 (mt) cc_final: 0.6961 (tt) REVERT: B 35 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6658 (tpt170) REVERT: B 114 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8058 (tttm) REVERT: B 144 TYR cc_start: 0.6227 (m-10) cc_final: 0.5904 (m-10) REVERT: A 107 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7110 (ptm160) REVERT: A 161 SER cc_start: 0.8375 (t) cc_final: 0.8122 (m) REVERT: A 200 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6353 (mt0) REVERT: A 214 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6065 (mp10) REVERT: A 299 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7613 (t0) REVERT: C 21 SER cc_start: 0.8003 (m) cc_final: 0.7737 (m) REVERT: C 41 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.7716 (m100) REVERT: C 295 MET cc_start: 0.7093 (mmt) cc_final: 0.6211 (mmt) outliers start: 57 outliers final: 31 residues processed: 161 average time/residue: 0.2272 time to fit residues: 49.2475 Evaluate side-chains 130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 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 299 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 359 ASN 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 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 323 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4524 r_free = 0.4524 target = 0.204224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.169808 restraints weight = 11114.466| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.42 r_work: 0.4038 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8803 Z= 0.444 Angle : 0.785 16.470 12023 Z= 0.415 Chirality : 0.048 0.182 1368 Planarity : 0.006 0.104 1407 Dihedral : 19.156 86.950 1406 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 6.63 % Allowed : 29.44 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.46 (0.25), residues: 955 helix: -1.12 (0.31), residues: 266 sheet: -2.80 (0.34), residues: 200 loop : -2.77 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 129 HIS 0.016 0.002 HIS C 66 PHE 0.024 0.002 PHE A 156 TYR 0.032 0.003 TYR A 300 ARG 0.022 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 159 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 100 time to evaluate : 0.846 Fit side-chains REVERT: F 17 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6441 (t80) REVERT: B 144 TYR cc_start: 0.6552 (m-80) cc_final: 0.6239 (m-10) REVERT: A 90 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6928 (t70) REVERT: A 102 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7637 (tp40) REVERT: A 214 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6114 (mp10) REVERT: A 396 LYS cc_start: 0.5104 (OUTLIER) cc_final: 0.4859 (ttmt) REVERT: C 21 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7739 (m) REVERT: C 41 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.7702 (m100) REVERT: C 81 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5743 (tt) REVERT: C 173 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6077 (mp) REVERT: C 295 MET cc_start: 0.7269 (mmt) cc_final: 0.6363 (mmt) REVERT: C 333 CYS cc_start: 0.5665 (OUTLIER) cc_final: 0.5130 (p) outliers start: 59 outliers final: 42 residues processed: 152 average time/residue: 0.2164 time to fit residues: 44.4013 Evaluate side-chains 142 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 90 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 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 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 237 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 144 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.214892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180498 restraints weight = 11131.310| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.49 r_work: 0.4095 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8803 Z= 0.223 Angle : 0.652 13.467 12023 Z= 0.342 Chirality : 0.043 0.163 1368 Planarity : 0.005 0.121 1407 Dihedral : 18.912 88.163 1404 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 5.96 % Allowed : 30.34 % Favored : 63.71 % 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: -3.22 (0.25), residues: 955 helix: -0.68 (0.32), residues: 261 sheet: -2.81 (0.33), residues: 200 loop : -2.69 (0.25), residues: 494 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 0.016 0.001 PHE A 156 TYR 0.019 0.002 TYR A 300 ARG 0.022 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 162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.843 Fit side-chains REVERT: F 41 ILE cc_start: 0.7464 (mt) cc_final: 0.6972 (tt) REVERT: B 35 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6367 (tpt170) REVERT: B 114 LYS cc_start: 0.8414 (tttm) cc_final: 0.8023 (tttm) REVERT: B 144 TYR cc_start: 0.6445 (m-80) cc_final: 0.6141 (m-10) REVERT: A 214 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6137 (mp10) REVERT: A 241 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6247 (mm) REVERT: C 21 SER cc_start: 0.7955 (OUTLIER) cc_final: 0.7677 (m) REVERT: C 41 TRP cc_start: 0.8031 (OUTLIER) cc_final: 0.7761 (m100) REVERT: C 81 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5644 (tt) REVERT: C 295 MET cc_start: 0.7090 (mmt) cc_final: 0.6328 (mmt) outliers start: 53 outliers final: 38 residues processed: 152 average time/residue: 0.2171 time to fit residues: 44.9562 Evaluate side-chains 140 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 220 LEU 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 90 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 241 LEU 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 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 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 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: 2.9990 chunk 83 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 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 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.217379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.185419 restraints weight = 11288.608| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.28 r_work: 0.4132 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8803 Z= 0.185 Angle : 0.621 11.784 12023 Z= 0.326 Chirality : 0.042 0.182 1368 Planarity : 0.004 0.044 1407 Dihedral : 18.769 89.586 1402 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 6.07 % Allowed : 29.89 % Favored : 64.04 % 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: -3.00 (0.26), residues: 955 helix: -0.38 (0.34), residues: 259 sheet: -2.57 (0.33), residues: 215 loop : -2.66 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 129 HIS 0.018 0.001 HIS C 156 PHE 0.028 0.001 PHE C 288 TYR 0.017 0.001 TYR A 300 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 162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 1.769 Fit side-chains REVERT: F 26 ARG cc_start: 0.5695 (ptt90) cc_final: 0.5459 (ptt180) REVERT: F 41 ILE cc_start: 0.7172 (mt) cc_final: 0.6775 (tt) REVERT: B 35 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6419 (tpt170) REVERT: B 114 LYS cc_start: 0.8317 (tttm) cc_final: 0.7958 (tttm) REVERT: B 144 TYR cc_start: 0.6548 (m-80) cc_final: 0.6289 (m-10) REVERT: A 90 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6627 (t0) REVERT: A 102 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7454 (tp40) REVERT: A 107 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6945 (ptm160) REVERT: A 200 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6497 (mt0) REVERT: A 214 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.5988 (mp10) REVERT: A 241 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6197 (mm) REVERT: C 21 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7710 (m) REVERT: C 81 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5522 (tt) REVERT: C 173 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5779 (mp) REVERT: C 295 MET cc_start: 0.7103 (mmt) cc_final: 0.6345 (mmt) REVERT: C 333 CYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5404 (p) REVERT: C 343 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.5056 (tt) outliers start: 54 outliers final: 33 residues processed: 152 average time/residue: 0.2646 time to fit residues: 54.8708 Evaluate side-chains 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 179 LEU 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 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 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 241 LEU Chi-restraints excluded: chain A residue 245 TYR 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 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 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 333 CYS Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 381 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 45 optimal weight: 0.0170 chunk 9 optimal weight: 0.1980 chunk 41 optimal weight: 0.0040 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.2430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 274 GLN A 299 ASN C 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.216023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.183956 restraints weight = 11102.041| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.20 r_work: 0.4203 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8803 Z= 0.159 Angle : 0.601 10.026 12023 Z= 0.313 Chirality : 0.041 0.163 1368 Planarity : 0.004 0.041 1407 Dihedral : 18.598 88.691 1398 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 4.61 % Allowed : 31.35 % Favored : 64.04 % 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: -2.72 (0.26), residues: 955 helix: -0.14 (0.35), residues: 259 sheet: -2.29 (0.34), residues: 211 loop : -2.55 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 41 HIS 0.013 0.001 HIS C 156 PHE 0.027 0.001 PHE B 90 TYR 0.018 0.001 TYR C 56 ARG 0.004 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 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.116 Fit side-chains REVERT: F 41 ILE cc_start: 0.6934 (mt) cc_final: 0.6561 (tt) REVERT: B 35 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6358 (tpt170) REVERT: B 114 LYS cc_start: 0.8253 (tttm) cc_final: 0.7943 (tttm) REVERT: B 144 TYR cc_start: 0.6399 (m-80) cc_final: 0.6174 (m-10) REVERT: A 102 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: A 214 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6037 (mp10) REVERT: A 386 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: A 396 LYS cc_start: 0.5170 (OUTLIER) cc_final: 0.4896 (ttmt) REVERT: C 21 SER cc_start: 0.7943 (m) cc_final: 0.7677 (m) REVERT: C 295 MET cc_start: 0.7058 (mmt) cc_final: 0.6284 (mmt) REVERT: C 343 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4611 (tt) outliers start: 41 outliers final: 23 residues processed: 143 average time/residue: 0.2872 time to fit residues: 57.2959 Evaluate side-chains 128 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 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 194 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 220 LEU 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 214 GLN Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 274 GLN 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 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 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 343 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.3980 chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 274 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.217834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.182205 restraints weight = 11261.881| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.42 r_work: 0.4129 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8803 Z= 0.210 Angle : 0.636 10.425 12023 Z= 0.334 Chirality : 0.043 0.153 1368 Planarity : 0.004 0.042 1407 Dihedral : 18.581 88.302 1391 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.16 % Allowed : 31.57 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.79 (0.26), residues: 955 helix: -0.20 (0.34), residues: 261 sheet: -2.39 (0.34), residues: 217 loop : -2.56 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 41 HIS 0.014 0.001 HIS C 156 PHE 0.039 0.002 PHE A 156 TYR 0.015 0.001 TYR C 56 ARG 0.006 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.718 Fit side-chains REVERT: F 41 ILE cc_start: 0.6973 (mt) cc_final: 0.6526 (tt) REVERT: B 35 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6325 (tpt170) REVERT: B 114 LYS cc_start: 0.8240 (tttm) cc_final: 0.7880 (tttm) REVERT: B 144 TYR cc_start: 0.6585 (m-80) cc_final: 0.6297 (m-10) REVERT: A 90 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6664 (t0) REVERT: A 214 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6020 (mp10) REVERT: A 241 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6236 (mm) REVERT: A 396 LYS cc_start: 0.5159 (OUTLIER) cc_final: 0.4933 (ttmt) REVERT: C 21 SER cc_start: 0.8053 (m) cc_final: 0.7766 (m) REVERT: C 48 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7226 (m110) REVERT: C 295 MET cc_start: 0.7128 (mmt) cc_final: 0.6299 (mmt) REVERT: C 343 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4717 (tt) outliers start: 37 outliers final: 24 residues processed: 128 average time/residue: 0.3219 time to fit residues: 57.3975 Evaluate side-chains 130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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 6 LEU Chi-restraints excluded: chain A residue 90 ASP 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 241 LEU Chi-restraints excluded: chain A residue 274 GLN 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 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 48 ASN 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 343 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: 3.9990 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 65 optimal weight: 0.0030 overall best weight: 0.4328 ------------------------------------------------------------------------------- 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 C 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.220569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.185932 restraints weight = 11124.028| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.37 r_work: 0.4170 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3291 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= 0.167 Angle : 0.623 9.498 12023 Z= 0.325 Chirality : 0.042 0.193 1368 Planarity : 0.004 0.041 1407 Dihedral : 18.513 88.338 1391 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 3.93 % Allowed : 31.91 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.69 (0.26), residues: 955 helix: -0.09 (0.34), residues: 261 sheet: -2.35 (0.34), residues: 219 loop : -2.50 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 129 HIS 0.012 0.001 HIS C 156 PHE 0.035 0.001 PHE A 156 TYR 0.021 0.001 TYR A 275 ARG 0.003 0.000 ARG F 40 ********************** 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 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.925 Fit side-chains REVERT: F 41 ILE cc_start: 0.6801 (mt) cc_final: 0.6393 (tt) REVERT: B 35 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6370 (tpt170) REVERT: B 114 LYS cc_start: 0.8223 (tttm) cc_final: 0.7938 (tttm) REVERT: B 144 TYR cc_start: 0.6530 (m-80) cc_final: 0.6272 (m-10) REVERT: A 102 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7320 (tp40) REVERT: A 214 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6114 (mp10) REVERT: A 241 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6140 (mm) REVERT: A 396 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4890 (ttmt) REVERT: C 21 SER cc_start: 0.7927 (m) cc_final: 0.7665 (m) REVERT: C 48 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.7045 (m110) REVERT: C 295 MET cc_start: 0.7096 (mmt) cc_final: 0.6305 (mmt) REVERT: C 343 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4635 (tt) outliers start: 35 outliers final: 24 residues processed: 127 average time/residue: 0.2182 time to fit residues: 38.1378 Evaluate side-chains 127 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 221 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 TYR 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 359 ASN Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain C residue 48 ASN 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 343 LEU 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: 3.9990 chunk 87 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 94 optimal weight: 0.0050 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.3732 ------------------------------------------------------------------------------- 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 274 GLN A 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.221707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.187081 restraints weight = 11263.426| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.39 r_work: 0.4181 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3349 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= 0.163 Angle : 0.612 9.208 12023 Z= 0.319 Chirality : 0.042 0.240 1368 Planarity : 0.004 0.039 1407 Dihedral : 18.482 88.591 1391 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.60 % Allowed : 32.58 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.64 (0.26), residues: 955 helix: -0.03 (0.34), residues: 261 sheet: -2.32 (0.34), residues: 219 loop : -2.48 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 129 HIS 0.011 0.001 HIS C 156 PHE 0.034 0.001 PHE A 156 TYR 0.011 0.001 TYR A 275 ARG 0.006 0.000 ARG B 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.86 seconds wall clock time: 73 minutes 40.26 seconds (4420.26 seconds total)