Starting phenix.real_space_refine on Thu Jul 2 05:39:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zl_67434/07_2026/20zl_67434.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zl_67434/07_2026/20zl_67434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/20zl_67434/07_2026/20zl_67434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zl_67434/07_2026/20zl_67434.map" model { file = "/net/cci-nas-00/data/ceres_data/20zl_67434/07_2026/20zl_67434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zl_67434/07_2026/20zl_67434.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.045 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4385 2.51 5 N 1178 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6904 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2171 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 271} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1710 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2534 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.60, per 1000 atoms: 0.23 Number of scatterers: 6904 At special positions: 0 Unit cell: (94.0666, 92.6833, 117.583, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1293 8.00 N 1178 7.00 C 4385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.75 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 350.0 milliseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 47.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 59 through 89 Processing helix chain 'R' and resid 98 through 128 Proline residue: R 121 - end of helix removed outlier: 3.524A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 185 through 200 removed outlier: 3.623A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 207 removed outlier: 4.011A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET R 207 " --> pdb=" O MET R 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 207' Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.864A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 265 Processing helix chain 'R' and resid 295 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 365 removed outlier: 3.596A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 366 through 375 removed outlier: 4.095A pdb=" N ASN R 370 " --> pdb=" O LEU R 366 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.947A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.016A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.704A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.528A pdb=" N GLU A 238 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.769A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.875A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.753A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.535A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 191 removed outlier: 3.683A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 191 removed outlier: 3.683A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.581A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.954A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 3.736A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.550A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.805A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.783A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.063A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1198 1.32 - 1.44: 1847 1.44 - 1.57: 3918 1.57 - 1.69: 14 1.69 - 1.82: 64 Bond restraints: 7041 Sorted by residual: bond pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta sigma weight residual 1.530 1.662 -0.132 1.55e-02 4.16e+03 7.27e+01 bond pdb=" CE1 HIS B 183 " pdb=" NE2 HIS B 183 " ideal model delta sigma weight residual 1.321 1.259 0.062 1.00e-02 1.00e+04 3.86e+01 bond pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 1.530 1.613 -0.084 1.56e-02 4.11e+03 2.87e+01 bond pdb=" CA GLU R 332 " pdb=" C GLU R 332 " ideal model delta sigma weight residual 1.524 1.592 -0.068 1.32e-02 5.74e+03 2.63e+01 bond pdb=" CG HIS A 213 " pdb=" CD2 HIS A 213 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.44e+01 ... (remaining 7036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 8906 4.23 - 8.47: 572 8.47 - 12.70: 77 12.70 - 16.94: 14 16.94 - 21.17: 3 Bond angle restraints: 9572 Sorted by residual: angle pdb=" C SER R 330 " pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta sigma weight residual 109.51 130.68 -21.17 1.71e+00 3.42e-01 1.53e+02 angle pdb=" C GLU R 332 " pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 110.81 128.88 -18.07 1.60e+00 3.91e-01 1.28e+02 angle pdb=" CA PHE B 292 " pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 113.80 124.81 -11.01 1.00e+00 1.00e+00 1.21e+02 angle pdb=" CA ASP B 163 " pdb=" CB ASP B 163 " pdb=" CG ASP B 163 " ideal model delta sigma weight residual 112.60 123.31 -10.71 1.00e+00 1.00e+00 1.15e+02 angle pdb=" C ASP R 331 " pdb=" N GLU R 332 " pdb=" CA GLU R 332 " ideal model delta sigma weight residual 120.54 134.45 -13.91 1.35e+00 5.49e-01 1.06e+02 ... (remaining 9567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.60: 3977 31.60 - 63.21: 163 63.21 - 94.81: 15 94.81 - 126.42: 2 126.42 - 158.02: 2 Dihedral angle restraints: 4159 sinusoidal: 1548 harmonic: 2611 Sorted by residual: dihedral pdb=" C CYS B 103 " pdb=" N CYS B 103 " pdb=" CA CYS B 103 " pdb=" CB CYS B 103 " ideal model delta harmonic sigma weight residual -122.60 -102.68 -19.92 0 2.50e+00 1.60e-01 6.35e+01 dihedral pdb=" C GLU R 332 " pdb=" N GLU R 332 " pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta harmonic sigma weight residual -122.60 -141.41 18.81 0 2.50e+00 1.60e-01 5.66e+01 dihedral pdb=" N TYR R 364 " pdb=" C TYR R 364 " pdb=" CA TYR R 364 " pdb=" CB TYR R 364 " ideal model delta harmonic sigma weight residual 122.80 141.57 -18.77 0 2.50e+00 1.60e-01 5.64e+01 ... (remaining 4156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 893 0.158 - 0.317: 184 0.317 - 0.475: 39 0.475 - 0.633: 3 0.633 - 0.792: 2 Chirality restraints: 1121 Sorted by residual: chirality pdb=" CA TYR R 364 " pdb=" N TYR R 364 " pdb=" C TYR R 364 " pdb=" CB TYR R 364 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASP B 27 " pdb=" N ASP B 27 " pdb=" C ASP B 27 " pdb=" CB ASP B 27 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 1118 not shown) Planarity restraints: 1201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 251 " -0.714 9.50e-02 1.11e+02 3.28e-01 1.29e+02 pdb=" NE ARG B 251 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG B 251 " 0.149 2.00e-02 2.50e+03 pdb=" NH1 ARG B 251 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG B 251 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " 0.489 9.50e-02 1.11e+02 2.25e-01 6.02e+01 pdb=" NE ARG B 150 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " -0.102 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 372 " -0.467 9.50e-02 1.11e+02 2.16e-01 5.95e+01 pdb=" NE ARG R 372 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG R 372 " 0.104 2.00e-02 2.50e+03 pdb=" NH1 ARG R 372 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG R 372 " -0.048 2.00e-02 2.50e+03 ... (remaining 1198 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 171 2.71 - 3.26: 6642 3.26 - 3.81: 11039 3.81 - 4.35: 14525 4.35 - 4.90: 23521 Nonbonded interactions: 55898 Sorted by model distance: nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.163 3.040 nonbonded pdb=" O ILE A 49 " pdb=" ND2 ASN A 331 " model vdw 2.272 3.120 nonbonded pdb=" OG SER R 52 " pdb=" N GLU R 53 " model vdw 2.301 3.120 nonbonded pdb=" O ASP R 112 " pdb=" OG1 THR R 115 " model vdw 2.371 3.040 nonbonded pdb=" C SER R 52 " pdb=" OG SER R 52 " model vdw 2.383 2.616 ... (remaining 55893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 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 : 0.015 0.718 7042 Z= 0.879 Angle : 2.522 51.433 9574 Z= 1.616 Chirality : 0.139 0.792 1121 Planarity : 0.019 0.328 1201 Dihedral : 17.661 158.019 2460 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.79 % Allowed : 11.98 % Favored : 82.23 % Cbeta Deviations : 4.25 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.25), residues: 877 helix: 0.27 (0.24), residues: 370 sheet: -1.74 (0.44), residues: 122 loop : -1.94 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.140 0.013 ARG B 251 TYR 0.064 0.010 TYR A 296 PHE 0.070 0.008 PHE A 191 TRP 0.064 0.012 TRP B 99 HIS 0.037 0.010 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.01221 / 0.77 ( 7041) covalent geometry : angle 2.45439 / 1.59 ( 9572) SS BOND : bond 0.71797 / 47.86 ( 1) SS BOND : angle 40.20890 / 27.50 ( 2) hydrogen bonds : bond 0.19463 / 13.43 ( 374) hydrogen bonds : angle 7.57770 / 5.72 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 239 VAL cc_start: 0.4869 (OUTLIER) cc_final: 0.4336 (p) REVERT: R 263 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7353 (tp) REVERT: A 246 SER cc_start: 0.7782 (m) cc_final: 0.7567 (m) REVERT: A 285 ILE cc_start: 0.7964 (mt) cc_final: 0.7705 (mt) REVERT: A 314 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7385 (tppt) REVERT: B 47 THR cc_start: 0.7876 (m) cc_final: 0.7002 (p) REVERT: B 241 PHE cc_start: 0.5665 (p90) cc_final: 0.5421 (p90) outliers start: 42 outliers final: 8 residues processed: 238 average time/residue: 0.0874 time to fit residues: 27.3705 Evaluate side-chains 128 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 102 HIS R 126 ASN R 240 ASN R 256 ASN R 296 GLN R 360 ASN R 370 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 331 ASN A 333 GLN B 6 GLN B 88 ASN B 119 ASN B 125 ASN B 183 HIS B 293 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.162569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.141411 restraints weight = 22407.735| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 4.12 r_work: 0.4320 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7042 Z= 0.211 Angle : 0.806 9.758 9574 Z= 0.432 Chirality : 0.046 0.245 1121 Planarity : 0.004 0.032 1201 Dihedral : 11.432 171.918 988 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.23 % Allowed : 17.63 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 877 helix: 1.33 (0.24), residues: 368 sheet: -1.33 (0.42), residues: 145 loop : -1.56 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.020 0.002 TYR B 59 PHE 0.029 0.003 PHE A 307 TRP 0.028 0.002 TRP B 297 HIS 0.011 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 ( 7041) covalent geometry : angle 0.80346 / 0.43 ( 9572) SS BOND : bond 0.00390 / 0.26 ( 1) SS BOND : angle 4.49508 / 2.68 ( 2) hydrogen bonds : bond 0.05463 / 3.77 ( 374) hydrogen bonds : angle 5.58877 / 4.18 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 263 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6862 (mt) REVERT: R 325 MET cc_start: 0.6865 (tmm) cc_final: 0.6564 (ppp) REVERT: R 347 MET cc_start: 0.8018 (mtt) cc_final: 0.7095 (mmm) REVERT: A 201 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7254 (p) REVERT: A 285 ILE cc_start: 0.7972 (mt) cc_final: 0.7706 (mt) REVERT: B 32 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7147 (pp30) REVERT: B 59 TYR cc_start: 0.6122 (m-10) cc_final: 0.5671 (m-10) REVERT: B 125 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7301 (p0) REVERT: B 142 HIS cc_start: 0.7077 (p90) cc_final: 0.6224 (p90) REVERT: B 232 ILE cc_start: 0.7409 (tt) cc_final: 0.7172 (mt) REVERT: B 241 PHE cc_start: 0.6256 (p90) cc_final: 0.5898 (p90) REVERT: C 38 MET cc_start: 0.4943 (ttt) cc_final: 0.4543 (ttt) outliers start: 38 outliers final: 12 residues processed: 159 average time/residue: 0.0664 time to fit residues: 14.7917 Evaluate side-chains 127 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 47 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 296 GLN ** R 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 370 ASN A 195 HIS A 213 HIS A 304 GLN A 322 HIS B 16 ASN B 119 ASN B 125 ASN B 340 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.163398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.143040 restraints weight = 21917.841| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 4.09 r_work: 0.4354 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7042 Z= 0.147 Angle : 0.710 11.078 9574 Z= 0.370 Chirality : 0.043 0.201 1121 Planarity : 0.004 0.056 1201 Dihedral : 10.489 174.331 972 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.41 % Allowed : 19.28 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 877 helix: 1.40 (0.25), residues: 381 sheet: -1.19 (0.40), residues: 149 loop : -1.45 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 323 TYR 0.021 0.002 TYR R 153 PHE 0.030 0.002 PHE R 345 TRP 0.043 0.002 TRP A 258 HIS 0.012 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 7041) covalent geometry : angle 0.70776 / 0.37 ( 9572) SS BOND : bond 0.00503 / 0.34 ( 1) SS BOND : angle 3.52869 / 2.24 ( 2) hydrogen bonds : bond 0.04689 / 3.22 ( 374) hydrogen bonds : angle 5.36461 / 3.99 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: R 153 TYR cc_start: 0.8588 (m-80) cc_final: 0.8387 (m-80) REVERT: R 263 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6754 (mp) REVERT: R 298 LEU cc_start: 0.8442 (mm) cc_final: 0.8044 (tp) REVERT: R 325 MET cc_start: 0.6557 (tmm) cc_final: 0.6309 (ppp) REVERT: R 347 MET cc_start: 0.7784 (mtt) cc_final: 0.6824 (mmm) REVERT: R 370 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: A 227 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5368 (mt) REVERT: A 247 MET cc_start: 0.6772 (mmt) cc_final: 0.6307 (mmt) REVERT: B 32 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7318 (pp30) REVERT: B 59 TYR cc_start: 0.6190 (m-10) cc_final: 0.5770 (m-80) REVERT: B 123 ILE cc_start: 0.8136 (mp) cc_final: 0.7506 (mp) REVERT: B 142 HIS cc_start: 0.6962 (p90) cc_final: 0.6319 (p-80) outliers start: 32 outliers final: 16 residues processed: 144 average time/residue: 0.0569 time to fit residues: 12.0753 Evaluate side-chains 133 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 18 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 14 optimal weight: 40.0000 chunk 62 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 296 GLN ** R 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.154479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.131788 restraints weight = 22043.654| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 3.88 r_work: 0.4172 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 7042 Z= 0.290 Angle : 0.819 9.953 9574 Z= 0.436 Chirality : 0.047 0.220 1121 Planarity : 0.005 0.065 1201 Dihedral : 10.258 171.792 971 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.41 % Allowed : 20.52 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.28), residues: 877 helix: 1.13 (0.26), residues: 372 sheet: -1.51 (0.39), residues: 164 loop : -1.27 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 15 TYR 0.023 0.003 TYR A 302 PHE 0.022 0.003 PHE C 61 TRP 0.032 0.003 TRP B 297 HIS 0.011 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.29 ( 7041) covalent geometry : angle 0.81538 / 0.43 ( 9572) SS BOND : bond 0.01949 / 1.30 ( 1) SS BOND : angle 5.18613 / 3.45 ( 2) hydrogen bonds : bond 0.05178 / 3.52 ( 374) hydrogen bonds : angle 5.77522 / 4.30 ( 1113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 153 TYR cc_start: 0.8694 (m-80) cc_final: 0.8407 (m-80) REVERT: R 158 ASN cc_start: 0.7981 (m-40) cc_final: 0.7503 (m-40) REVERT: R 325 MET cc_start: 0.7074 (tmm) cc_final: 0.6768 (ppp) REVERT: R 347 MET cc_start: 0.8012 (mtt) cc_final: 0.7139 (mmm) REVERT: B 16 ASN cc_start: 0.5900 (m-40) cc_final: 0.5620 (m110) REVERT: B 111 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7917 (t80) REVERT: B 123 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7390 (mp) REVERT: B 127 LYS cc_start: 0.8339 (mttp) cc_final: 0.7974 (mmtt) REVERT: B 155 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6581 (t0) REVERT: B 222 PHE cc_start: 0.6557 (m-80) cc_final: 0.6320 (m-80) REVERT: B 239 ASN cc_start: 0.7642 (t0) cc_final: 0.7422 (t0) REVERT: B 321 THR cc_start: 0.5474 (p) cc_final: 0.5073 (p) outliers start: 32 outliers final: 15 residues processed: 151 average time/residue: 0.0603 time to fit residues: 13.2830 Evaluate side-chains 143 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 85 optimal weight: 0.0970 chunk 37 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 343 HIS A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.156690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.133936 restraints weight = 21577.822| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 4.03 r_work: 0.4207 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7042 Z= 0.189 Angle : 0.723 9.272 9574 Z= 0.377 Chirality : 0.044 0.202 1121 Planarity : 0.004 0.066 1201 Dihedral : 9.881 168.413 968 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.86 % Allowed : 23.28 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.28), residues: 877 helix: 1.22 (0.26), residues: 373 sheet: -1.56 (0.38), residues: 170 loop : -1.28 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 322 TYR 0.033 0.002 TYR B 85 PHE 0.012 0.002 PHE R 312 TRP 0.023 0.002 TRP B 297 HIS 0.008 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 7041) covalent geometry : angle 0.72038 / 0.38 ( 9572) SS BOND : bond 0.01072 / 0.71 ( 1) SS BOND : angle 4.24027 / 2.84 ( 2) hydrogen bonds : bond 0.04509 / 3.06 ( 374) hydrogen bonds : angle 5.53583 / 4.07 ( 1113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 153 TYR cc_start: 0.8787 (m-80) cc_final: 0.8507 (m-80) REVERT: R 325 MET cc_start: 0.7172 (tmm) cc_final: 0.6723 (ppp) REVERT: R 347 MET cc_start: 0.7922 (mtt) cc_final: 0.6696 (mpp) REVERT: A 227 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5609 (mt) REVERT: A 243 MET cc_start: 0.6909 (ttp) cc_final: 0.6391 (ppp) REVERT: B 16 ASN cc_start: 0.5579 (m-40) cc_final: 0.5316 (m110) REVERT: B 111 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7697 (t80) REVERT: B 123 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 125 ASN cc_start: 0.7996 (p0) cc_final: 0.7777 (p0) REVERT: B 127 LYS cc_start: 0.8376 (mttp) cc_final: 0.7986 (mmtt) REVERT: B 132 ASN cc_start: 0.6960 (p0) cc_final: 0.6660 (t0) REVERT: B 155 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6924 (t0) outliers start: 28 outliers final: 18 residues processed: 141 average time/residue: 0.0538 time to fit residues: 11.0512 Evaluate side-chains 139 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 239 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.158532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.136353 restraints weight = 21689.332| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 4.09 r_work: 0.4237 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7042 Z= 0.143 Angle : 0.687 10.971 9574 Z= 0.353 Chirality : 0.043 0.187 1121 Planarity : 0.004 0.077 1201 Dihedral : 9.653 167.867 968 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.99 % Allowed : 23.42 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 877 helix: 1.25 (0.26), residues: 382 sheet: -1.46 (0.39), residues: 159 loop : -1.24 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 322 TYR 0.021 0.001 TYR B 59 PHE 0.016 0.002 PHE R 205 TRP 0.021 0.002 TRP B 297 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7041) covalent geometry : angle 0.68567 / 0.35 ( 9572) SS BOND : bond 0.00588 / 0.39 ( 1) SS BOND : angle 3.52137 / 2.29 ( 2) hydrogen bonds : bond 0.04128 / 2.85 ( 374) hydrogen bonds : angle 5.29106 / 3.92 ( 1113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: R 205 PHE cc_start: 0.7231 (p90) cc_final: 0.6937 (p90) REVERT: R 207 MET cc_start: 0.6431 (tpp) cc_final: 0.5846 (tpp) REVERT: R 325 MET cc_start: 0.7290 (tmm) cc_final: 0.6902 (ppp) REVERT: R 347 MET cc_start: 0.7786 (mtt) cc_final: 0.6584 (mpp) REVERT: R 370 ASN cc_start: 0.8280 (t0) cc_final: 0.7866 (m110) REVERT: A 227 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.6069 (mt) REVERT: A 243 MET cc_start: 0.7456 (ttp) cc_final: 0.6950 (ppp) REVERT: B 16 ASN cc_start: 0.5506 (m-40) cc_final: 0.5234 (m110) REVERT: B 51 LEU cc_start: 0.4010 (OUTLIER) cc_final: 0.3566 (mt) REVERT: B 132 ASN cc_start: 0.6969 (p0) cc_final: 0.6634 (t0) REVERT: B 155 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6472 (t0) REVERT: B 222 PHE cc_start: 0.6479 (m-80) cc_final: 0.6208 (m-80) REVERT: B 340 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.5578 (m-40) REVERT: C 21 MET cc_start: 0.8396 (tmm) cc_final: 0.8115 (tmm) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 0.0609 time to fit residues: 12.6801 Evaluate side-chains 135 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 155 ASN B 220 GLN B 239 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.159860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.138332 restraints weight = 21636.147| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 4.10 r_work: 0.4268 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7042 Z= 0.136 Angle : 0.679 9.608 9574 Z= 0.349 Chirality : 0.042 0.187 1121 Planarity : 0.004 0.059 1201 Dihedral : 9.413 168.451 968 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.13 % Allowed : 23.42 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 877 helix: 1.34 (0.27), residues: 383 sheet: -1.29 (0.42), residues: 147 loop : -1.25 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG R 142 TYR 0.028 0.002 TYR R 364 PHE 0.047 0.002 PHE R 345 TRP 0.017 0.002 TRP B 297 HIS 0.010 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 7041) covalent geometry : angle 0.67696 / 0.35 ( 9572) SS BOND : bond 0.00646 / 0.43 ( 1) SS BOND : angle 3.40973 / 2.09 ( 2) hydrogen bonds : bond 0.04132 / 2.89 ( 374) hydrogen bonds : angle 5.22942 / 3.81 ( 1113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: R 149 ASP cc_start: 0.8186 (t0) cc_final: 0.7868 (p0) REVERT: R 325 MET cc_start: 0.7265 (tmm) cc_final: 0.6848 (ppp) REVERT: R 347 MET cc_start: 0.7885 (mtt) cc_final: 0.6960 (mmm) REVERT: R 370 ASN cc_start: 0.7955 (t0) cc_final: 0.7476 (m110) REVERT: A 198 MET cc_start: 0.4711 (mmm) cc_final: 0.4461 (tpt) REVERT: A 227 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6078 (mt) REVERT: A 243 MET cc_start: 0.7434 (ttp) cc_final: 0.7208 (ppp) REVERT: A 296 TYR cc_start: 0.6055 (t80) cc_final: 0.4888 (t80) REVERT: B 16 ASN cc_start: 0.5462 (m-40) cc_final: 0.5166 (m110) REVERT: B 51 LEU cc_start: 0.3548 (OUTLIER) cc_final: 0.3198 (mt) REVERT: B 99 TRP cc_start: 0.7694 (m100) cc_final: 0.7175 (m100) REVERT: B 132 ASN cc_start: 0.6834 (p0) cc_final: 0.6530 (t0) REVERT: B 155 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6984 (t0) REVERT: B 340 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.5213 (m-40) REVERT: C 61 PHE cc_start: 0.2924 (m-10) cc_final: 0.2688 (m-10) outliers start: 30 outliers final: 17 residues processed: 136 average time/residue: 0.0561 time to fit residues: 11.3207 Evaluate side-chains 130 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 75 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 155 ASN B 220 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.157937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.135781 restraints weight = 22009.710| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 3.90 r_work: 0.4232 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7042 Z= 0.163 Angle : 0.709 10.171 9574 Z= 0.362 Chirality : 0.043 0.187 1121 Planarity : 0.004 0.062 1201 Dihedral : 9.229 168.113 968 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.72 % Allowed : 24.10 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.29), residues: 877 helix: 1.36 (0.27), residues: 382 sheet: -1.58 (0.38), residues: 173 loop : -1.19 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 142 TYR 0.027 0.002 TYR B 59 PHE 0.036 0.002 PHE R 345 TRP 0.021 0.002 TRP B 297 HIS 0.008 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 7041) covalent geometry : angle 0.70579 / 0.36 ( 9572) SS BOND : bond 0.00963 / 0.64 ( 1) SS BOND : angle 4.66197 / 3.08 ( 2) hydrogen bonds : bond 0.04144 / 2.84 ( 374) hydrogen bonds : angle 5.27577 / 3.85 ( 1113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: R 116 LEU cc_start: 0.8579 (mp) cc_final: 0.8278 (pp) REVERT: R 149 ASP cc_start: 0.8155 (t0) cc_final: 0.7765 (p0) REVERT: R 158 ASN cc_start: 0.8213 (t0) cc_final: 0.7423 (t0) REVERT: R 325 MET cc_start: 0.7361 (tmm) cc_final: 0.6946 (ppp) REVERT: R 347 MET cc_start: 0.7891 (mtt) cc_final: 0.7016 (mmm) REVERT: R 370 ASN cc_start: 0.7882 (t0) cc_final: 0.7559 (m-40) REVERT: A 243 MET cc_start: 0.6791 (ttp) cc_final: 0.6560 (ppp) REVERT: B 51 LEU cc_start: 0.4064 (OUTLIER) cc_final: 0.3619 (mt) REVERT: B 99 TRP cc_start: 0.7728 (m100) cc_final: 0.7341 (m100) REVERT: B 155 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7271 (t0) REVERT: B 239 ASN cc_start: 0.6972 (t0) cc_final: 0.6557 (t0) REVERT: B 340 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.5018 (m-40) outliers start: 27 outliers final: 19 residues processed: 130 average time/residue: 0.0606 time to fit residues: 11.7168 Evaluate side-chains 128 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.154670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.133056 restraints weight = 21676.438| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 4.09 r_work: 0.4165 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.8299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7042 Z= 0.237 Angle : 0.781 10.165 9574 Z= 0.403 Chirality : 0.045 0.196 1121 Planarity : 0.005 0.077 1201 Dihedral : 9.376 162.810 968 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.72 % Allowed : 25.07 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.28), residues: 877 helix: 1.18 (0.26), residues: 379 sheet: -1.98 (0.35), residues: 187 loop : -1.18 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 142 TYR 0.044 0.003 TYR R 153 PHE 0.034 0.003 PHE R 345 TRP 0.024 0.002 TRP B 297 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 ( 7041) covalent geometry : angle 0.77731 / 0.40 ( 9572) SS BOND : bond 0.01249 / 0.83 ( 1) SS BOND : angle 5.21415 / 3.53 ( 2) hydrogen bonds : bond 0.04454 / 3.01 ( 374) hydrogen bonds : angle 5.49212 / 4.01 ( 1113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 LEU cc_start: 0.8627 (mp) cc_final: 0.8350 (pp) REVERT: R 149 ASP cc_start: 0.7997 (t0) cc_final: 0.7484 (t0) REVERT: R 158 ASN cc_start: 0.8318 (t0) cc_final: 0.7702 (t0) REVERT: R 325 MET cc_start: 0.7477 (tmm) cc_final: 0.7051 (ppp) REVERT: R 347 MET cc_start: 0.7948 (mtt) cc_final: 0.7090 (mmm) REVERT: R 370 ASN cc_start: 0.8154 (t0) cc_final: 0.7824 (m-40) REVERT: B 51 LEU cc_start: 0.4453 (OUTLIER) cc_final: 0.4000 (mt) REVERT: B 155 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7351 (t0) REVERT: B 170 ASP cc_start: 0.7042 (t70) cc_final: 0.6474 (t70) REVERT: B 239 ASN cc_start: 0.7670 (t0) cc_final: 0.7333 (t0) REVERT: B 340 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.5829 (m-40) outliers start: 27 outliers final: 19 residues processed: 131 average time/residue: 0.0579 time to fit residues: 10.9980 Evaluate side-chains 132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 331 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.156827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.135159 restraints weight = 22216.717| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 4.28 r_work: 0.4212 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7042 Z= 0.158 Angle : 0.742 9.725 9574 Z= 0.381 Chirality : 0.044 0.217 1121 Planarity : 0.005 0.067 1201 Dihedral : 9.123 161.470 968 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.03 % Allowed : 26.45 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.28), residues: 877 helix: 1.18 (0.26), residues: 381 sheet: -1.73 (0.38), residues: 171 loop : -1.29 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 142 TYR 0.040 0.002 TYR R 153 PHE 0.032 0.002 PHE R 345 TRP 0.048 0.002 TRP B 99 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7041) covalent geometry : angle 0.73946 / 0.38 ( 9572) SS BOND : bond 0.01202 / 0.80 ( 1) SS BOND : angle 4.44805 / 2.97 ( 2) hydrogen bonds : bond 0.04150 / 2.86 ( 374) hydrogen bonds : angle 5.39984 / 3.94 ( 1113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 LEU cc_start: 0.8525 (mp) cc_final: 0.8300 (pp) REVERT: R 149 ASP cc_start: 0.8002 (t0) cc_final: 0.7467 (t0) REVERT: R 158 ASN cc_start: 0.8177 (t0) cc_final: 0.7607 (t0) REVERT: R 325 MET cc_start: 0.7053 (tmm) cc_final: 0.6697 (ppp) REVERT: R 347 MET cc_start: 0.7925 (mtt) cc_final: 0.7069 (mmm) REVERT: R 370 ASN cc_start: 0.7927 (t0) cc_final: 0.7676 (t0) REVERT: A 261 ASP cc_start: 0.7564 (p0) cc_final: 0.7242 (p0) REVERT: A 345 LYS cc_start: 0.6756 (mttp) cc_final: 0.6487 (mtmt) REVERT: B 155 ASN cc_start: 0.7460 (OUTLIER) cc_final: 0.6864 (t0) REVERT: B 170 ASP cc_start: 0.6874 (t70) cc_final: 0.6424 (t70) REVERT: B 273 ILE cc_start: 0.5722 (mm) cc_final: 0.5289 (mm) REVERT: B 340 ASN cc_start: 0.6992 (OUTLIER) cc_final: 0.5895 (m-40) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 0.0664 time to fit residues: 11.5778 Evaluate side-chains 124 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.154983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.132553 restraints weight = 22025.880| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 3.68 r_work: 0.4193 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.8714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7042 Z= 0.200 Angle : 0.758 9.661 9574 Z= 0.391 Chirality : 0.044 0.182 1121 Planarity : 0.005 0.067 1201 Dihedral : 9.123 159.825 968 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.17 % Allowed : 26.58 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.28), residues: 877 helix: 1.23 (0.26), residues: 376 sheet: -1.72 (0.37), residues: 167 loop : -1.37 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 142 TYR 0.042 0.002 TYR R 153 PHE 0.028 0.002 PHE R 345 TRP 0.043 0.003 TRP B 99 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 7041) covalent geometry : angle 0.75431 / 0.39 ( 9572) SS BOND : bond 0.01138 / 0.76 ( 1) SS BOND : angle 5.17319 / 3.50 ( 2) hydrogen bonds : bond 0.04261 / 2.90 ( 374) hydrogen bonds : angle 5.42976 / 3.96 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.88 seconds wall clock time: 35 minutes 30.61 seconds (2130.61 seconds total)