Starting phenix.real_space_refine on Thu Jul 2 16:35:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.map" model { file = "/net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8csx_26974/07_2026/8csx_26974.cif" } resolution = 2.4 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= 0.003 sd= 0.322 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5941 2.51 5 N 1424 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 9116 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 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: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 43 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.53 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.47 Time building chain proxies: 1.80, per 1000 atoms: 0.20 Number of scatterers: 9116 At special positions: 0 Unit cell: (91.3, 89.64, 92.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1685 8.00 N 1424 7.00 C 5941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 315.5 milliseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 79.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'K' and resid 11 through 31 Processing helix chain 'K' and resid 43 through 60 removed outlier: 3.889A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 66 removed outlier: 3.872A pdb=" N THR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 removed outlier: 3.647A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU K 93 " --> pdb=" O GLN K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 removed outlier: 3.592A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 162 Processing helix chain 'K' and resid 166 through 170 removed outlier: 3.562A pdb=" N LEU K 169 " --> pdb=" O HIS K 166 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 170' Processing helix chain 'K' and resid 171 through 187 removed outlier: 3.569A pdb=" N CYS K 186 " --> pdb=" O THR K 182 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU K 187 " --> pdb=" O VAL K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 225 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 230 through 256 Processing helix chain 'K' and resid 266 through 274 removed outlier: 3.628A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 282 Processing helix chain 'K' and resid 290 through 312 removed outlier: 3.701A pdb=" N ALA K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 350 removed outlier: 3.602A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 389 Processing helix chain 'K' and resid 390 through 394 Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.714A pdb=" N TYR K 401 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 Processing helix chain 'L' and resid 3 through 23 Processing helix chain 'L' and resid 50 through 63 Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 75 through 104 removed outlier: 3.739A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 133 removed outlier: 3.711A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 162 removed outlier: 3.639A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 191 through 195 Processing helix chain 'L' and resid 204 through 228 removed outlier: 3.743A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 233 through 261 removed outlier: 3.714A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 266 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.657A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 321 removed outlier: 4.546A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 329 through 334 Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 357 through 384 Processing helix chain 'L' and resid 398 through 402 removed outlier: 3.619A pdb=" N VAL L 401 " --> pdb=" O ASP L 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 23 Processing helix chain 'Q' and resid 47 through 63 Proline residue: Q 52 - end of helix Processing helix chain 'Q' and resid 63 through 69 removed outlier: 3.621A pdb=" N MET Q 69 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 72 No H-bonds generated for 'chain 'Q' and resid 70 through 72' Processing helix chain 'Q' and resid 75 through 104 removed outlier: 3.812A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 133 removed outlier: 3.507A pdb=" N MET Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 162 removed outlier: 3.688A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 189 Processing helix chain 'Q' and resid 191 through 195 Processing helix chain 'Q' and resid 204 through 228 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 233 through 262 removed outlier: 3.716A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 266 Processing helix chain 'Q' and resid 268 through 275 Processing helix chain 'Q' and resid 277 through 283 Processing helix chain 'Q' and resid 292 through 321 removed outlier: 4.513A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 329 through 334 Processing helix chain 'Q' and resid 335 through 351 Processing helix chain 'Q' and resid 357 through 385 removed outlier: 4.028A pdb=" N LEU Q 385 " --> pdb=" O LEU Q 381 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 402 removed outlier: 3.583A pdb=" N VAL Q 401 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.923A pdb=" N HIS K 33 " --> pdb=" O ILE K 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AA3, first strand: chain 'Q' and resid 24 through 25 658 hydrogen bonds defined for protein. 1933 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: 1.29 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.44: 2492 1.44 - 1.57: 5177 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9199 Sorted by residual: bond pdb=" C PRO Q 293 " pdb=" O PRO Q 293 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" N VAL Q 373 " pdb=" CA VAL Q 373 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.02e+00 bond pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.97e+00 bond pdb=" N LEU Q 383 " pdb=" CA LEU Q 383 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.28e-02 6.10e+03 7.70e+00 bond pdb=" N ILE Q 188 " pdb=" CA ILE Q 188 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.13e+00 ... (remaining 9194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12044 1.85 - 3.70: 417 3.70 - 5.56: 51 5.56 - 7.41: 12 7.41 - 9.26: 4 Bond angle restraints: 12528 Sorted by residual: angle pdb=" N LEU Q 189 " pdb=" CA LEU Q 189 " pdb=" C LEU Q 189 " ideal model delta sigma weight residual 113.02 107.62 5.40 1.20e+00 6.94e-01 2.03e+01 angle pdb=" N ALA Q 353 " pdb=" CA ALA Q 353 " pdb=" C ALA Q 353 " ideal model delta sigma weight residual 111.28 106.39 4.89 1.09e+00 8.42e-01 2.01e+01 angle pdb=" C ARG Q 323 " pdb=" N ILE Q 324 " pdb=" CA ILE Q 324 " ideal model delta sigma weight residual 123.12 117.34 5.78 1.30e+00 5.92e-01 1.98e+01 angle pdb=" CA TYR Q 180 " pdb=" C TYR Q 180 " pdb=" O TYR Q 180 " ideal model delta sigma weight residual 120.55 116.12 4.43 1.06e+00 8.90e-01 1.75e+01 angle pdb=" C TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta sigma weight residual 110.79 117.41 -6.62 1.66e+00 3.63e-01 1.59e+01 ... (remaining 12523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 4974 24.16 - 48.32: 214 48.32 - 72.48: 31 72.48 - 96.64: 4 96.64 - 120.80: 1 Dihedral angle restraints: 5224 sinusoidal: 1930 harmonic: 3294 Sorted by residual: dihedral pdb=" C TYR Q 180 " pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta harmonic sigma weight residual -122.60 -134.06 11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" C02 AJP Q 501 " pdb=" C85 AJP Q 501 " pdb=" O84 AJP Q 501 " pdb=" C05 AJP Q 501 " ideal model delta sinusoidal sigma weight residual -57.60 63.20 -120.80 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA TRP Q 403 " pdb=" C TRP Q 403 " pdb=" N LYS Q 404 " pdb=" CA LYS Q 404 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1263 0.067 - 0.134: 197 0.134 - 0.202: 22 0.202 - 0.269: 7 0.269 - 0.336: 2 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA TYR Q 180 " pdb=" N TYR Q 180 " pdb=" C TYR Q 180 " pdb=" CB TYR Q 180 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C11 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" C12 AJP Q 501 " pdb=" C16 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C08 AJP Q 502 " pdb=" C07 AJP Q 502 " pdb=" C10 AJP Q 502 " pdb=" O09 AJP Q 502 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1488 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 384 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C LYS Q 384 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS Q 384 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU Q 385 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 324 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C ILE Q 324 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE Q 324 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS Q 325 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 345 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C GLY Q 345 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY Q 345 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE Q 346 " -0.013 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1044 2.75 - 3.28: 9611 3.28 - 3.82: 17718 3.82 - 4.36: 21251 4.36 - 4.90: 35084 Nonbonded interactions: 84708 Sorted by model distance: nonbonded pdb=" OD2 ASP Q 399 " pdb=" O HOH Q 601 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASP Q 398 " pdb=" OG SER Q 400 " model vdw 2.226 3.040 nonbonded pdb=" O TYR K 178 " pdb=" OG1 THR K 182 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR L 408 " pdb=" O HOH L 601 " model vdw 2.242 3.040 nonbonded pdb=" O LYS L 404 " pdb=" O HOH L 602 " model vdw 2.266 3.040 ... (remaining 84703 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 Found NCS groups: ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } 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=0.45 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: 1.350 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: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.770 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 : 0.006 0.049 9199 Z= 0.307 Angle : 0.787 9.260 12528 Z= 0.483 Chirality : 0.053 0.336 1491 Planarity : 0.006 0.055 1505 Dihedral : 13.618 120.799 3120 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.67 % Favored : 98.24 % Rotamer: Outliers : 3.86 % Allowed : 5.58 % Favored : 90.56 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.24), residues: 1143 helix: 1.68 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 191 TYR 0.027 0.003 TYR Q 180 PHE 0.021 0.003 PHE L 54 TRP 0.012 0.002 TRP K 16 HIS 0.006 0.002 HIS Q 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.31 ( 9199) covalent geometry : angle 0.78690 / 0.48 (12528) hydrogen bonds : bond 0.12699 / 8.44 ( 658) hydrogen bonds : angle 5.93847 / 4.31 ( 1933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.257 Fit side-chains REVERT: K 11 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6807 (mtm-85) REVERT: K 16 TRP cc_start: 0.7806 (OUTLIER) cc_final: 0.5828 (t-100) REVERT: K 100 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.4697 (tp-100) REVERT: K 201 ARG cc_start: 0.8316 (mmt180) cc_final: 0.7921 (tpp-160) REVERT: K 329 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6211 (m-70) REVERT: K 364 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6714 (mm) REVERT: K 382 LEU cc_start: 0.8329 (mt) cc_final: 0.7832 (tp) REVERT: K 390 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7760 (mp) REVERT: L 2 ARG cc_start: 0.7458 (ptt90) cc_final: 0.7235 (ptt180) REVERT: L 199 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: L 202 GLU cc_start: 0.7898 (tt0) cc_final: 0.7632 (tt0) REVERT: L 305 MET cc_start: 0.8291 (ttm) cc_final: 0.8054 (ttp) REVERT: Q 196 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7370 (mmtt) REVERT: Q 231 GLU cc_start: 0.7068 (tp30) cc_final: 0.6561 (tp30) outliers start: 36 outliers final: 9 residues processed: 233 average time/residue: 0.4637 time to fit residues: 115.3099 Evaluate side-chains 198 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 302 ILE Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 384 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN K 49 GLN K 260 HIS L 58 HIS L 263 HIS Q 55 GLN Q 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.094782 restraints weight = 16387.497| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.37 r_work: 0.2799 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9199 Z= 0.207 Angle : 0.637 8.113 12528 Z= 0.340 Chirality : 0.044 0.147 1491 Planarity : 0.005 0.054 1505 Dihedral : 8.250 105.861 1282 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.85 % Favored : 98.07 % Rotamer: Outliers : 3.97 % Allowed : 10.19 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.24), residues: 1143 helix: 1.92 (0.17), residues: 806 sheet: None (None), residues: 0 loop : -0.09 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 238 TYR 0.022 0.003 TYR Q 244 PHE 0.022 0.002 PHE L 54 TRP 0.011 0.002 TRP K 16 HIS 0.005 0.001 HIS Q 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 ( 9199) covalent geometry : angle 0.63708 / 0.34 (12528) hydrogen bonds : bond 0.06751 / 4.46 ( 658) hydrogen bonds : angle 5.23336 / 3.85 ( 1933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.346 Fit side-chains REVERT: K 11 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7039 (mtt90) REVERT: K 100 GLN cc_start: 0.5535 (OUTLIER) cc_final: 0.4891 (tp-100) REVERT: K 201 ARG cc_start: 0.8307 (mmt180) cc_final: 0.7916 (tpp-160) REVERT: K 329 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.5903 (m-70) REVERT: K 382 LEU cc_start: 0.8299 (mt) cc_final: 0.7849 (tp) REVERT: L 199 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7131 (pm20) REVERT: L 202 GLU cc_start: 0.8285 (tt0) cc_final: 0.8062 (tt0) REVERT: L 305 MET cc_start: 0.8416 (ttm) cc_final: 0.8194 (ttp) REVERT: Q 196 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7523 (mppt) REVERT: Q 199 GLU cc_start: 0.7745 (pt0) cc_final: 0.7362 (pp20) REVERT: Q 231 GLU cc_start: 0.7210 (tp30) cc_final: 0.6663 (tp30) REVERT: Q 321 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7847 (mppt) REVERT: Q 323 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8009 (mtt-85) REVERT: Q 407 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7935 (tptp) outliers start: 37 outliers final: 15 residues processed: 201 average time/residue: 0.4389 time to fit residues: 94.5356 Evaluate side-chains 208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 407 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.114449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095385 restraints weight = 16118.162| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.32 r_work: 0.2813 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9199 Z= 0.195 Angle : 0.623 7.838 12528 Z= 0.331 Chirality : 0.043 0.163 1491 Planarity : 0.005 0.041 1505 Dihedral : 7.884 105.425 1272 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.76 % Allowed : 11.70 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.24), residues: 1143 helix: 1.97 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.13 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 154 TYR 0.022 0.003 TYR Q 244 PHE 0.021 0.002 PHE L 54 TRP 0.010 0.002 TRP K 16 HIS 0.005 0.001 HIS Q 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 9199) covalent geometry : angle 0.62262 / 0.33 (12528) hydrogen bonds : bond 0.06523 / 4.30 ( 658) hydrogen bonds : angle 5.15923 / 3.80 ( 1933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.394 Fit side-chains REVERT: K 11 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7068 (mtt90) REVERT: K 100 GLN cc_start: 0.5538 (OUTLIER) cc_final: 0.4983 (tp-100) REVERT: K 201 ARG cc_start: 0.8279 (mmt180) cc_final: 0.7924 (tpp-160) REVERT: K 329 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5863 (m-70) REVERT: K 364 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6685 (mm) REVERT: K 382 LEU cc_start: 0.8302 (mt) cc_final: 0.7846 (tp) REVERT: K 390 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7587 (mp) REVERT: L 199 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: L 202 GLU cc_start: 0.8286 (tt0) cc_final: 0.8059 (tt0) REVERT: L 305 MET cc_start: 0.8396 (ttm) cc_final: 0.8168 (ttp) REVERT: Q 196 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7507 (mppt) REVERT: Q 199 GLU cc_start: 0.7711 (pt0) cc_final: 0.7356 (pp20) REVERT: Q 231 GLU cc_start: 0.7209 (tp30) cc_final: 0.6670 (tp30) REVERT: Q 323 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7992 (mtt-85) REVERT: Q 407 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7948 (tppt) outliers start: 35 outliers final: 16 residues processed: 205 average time/residue: 0.4664 time to fit residues: 102.3153 Evaluate side-chains 209 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 407 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094145 restraints weight = 18641.888| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.40 r_work: 0.2793 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9199 Z= 0.212 Angle : 0.644 8.058 12528 Z= 0.341 Chirality : 0.044 0.159 1491 Planarity : 0.005 0.042 1505 Dihedral : 7.774 105.113 1268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.86 % Allowed : 11.70 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.23), residues: 1143 helix: 1.95 (0.17), residues: 806 sheet: None (None), residues: 0 loop : -0.18 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 154 TYR 0.021 0.003 TYR Q 244 PHE 0.022 0.002 PHE L 54 TRP 0.010 0.002 TRP K 16 HIS 0.005 0.001 HIS Q 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 ( 9199) covalent geometry : angle 0.64372 / 0.34 (12528) hydrogen bonds : bond 0.06721 / 4.43 ( 658) hydrogen bonds : angle 5.18213 / 3.82 ( 1933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.238 Fit side-chains REVERT: K 11 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7101 (mtt90) REVERT: K 100 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5050 (tp-100) REVERT: K 329 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5808 (m-70) REVERT: K 364 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6677 (mm) REVERT: K 382 LEU cc_start: 0.8311 (mt) cc_final: 0.7752 (tp) REVERT: K 390 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7578 (mp) REVERT: L 199 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: L 202 GLU cc_start: 0.8298 (tt0) cc_final: 0.8067 (tt0) REVERT: L 305 MET cc_start: 0.8417 (ttm) cc_final: 0.8178 (ttp) REVERT: Q 196 LYS cc_start: 0.7821 (mmmm) cc_final: 0.7342 (mmpt) REVERT: Q 199 GLU cc_start: 0.7728 (pt0) cc_final: 0.7365 (pp20) REVERT: Q 231 GLU cc_start: 0.7215 (tp30) cc_final: 0.6676 (tp30) REVERT: Q 323 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8011 (mtt-85) outliers start: 36 outliers final: 20 residues processed: 203 average time/residue: 0.4964 time to fit residues: 107.5019 Evaluate side-chains 217 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 407 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 112 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.096987 restraints weight = 14084.489| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.17 r_work: 0.2845 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9199 Z= 0.174 Angle : 0.594 7.563 12528 Z= 0.315 Chirality : 0.042 0.144 1491 Planarity : 0.005 0.041 1505 Dihedral : 7.569 105.315 1268 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.65 % Allowed : 12.34 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.24), residues: 1143 helix: 2.09 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.14 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 154 TYR 0.021 0.002 TYR Q 244 PHE 0.018 0.002 PHE L 54 TRP 0.010 0.002 TRP K 16 HIS 0.004 0.001 HIS Q 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 9199) covalent geometry : angle 0.59355 / 0.32 (12528) hydrogen bonds : bond 0.06161 / 4.06 ( 658) hydrogen bonds : angle 5.07666 / 3.75 ( 1933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.218 Fit side-chains REVERT: K 11 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7033 (mtt90) REVERT: K 16 TRP cc_start: 0.7624 (OUTLIER) cc_final: 0.5603 (t-100) REVERT: K 100 GLN cc_start: 0.5595 (OUTLIER) cc_final: 0.5071 (tp-100) REVERT: K 201 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7897 (tpp-160) REVERT: K 329 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5761 (m-70) REVERT: K 364 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6751 (mm) REVERT: K 382 LEU cc_start: 0.8298 (mt) cc_final: 0.7882 (tp) REVERT: K 390 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7580 (mp) REVERT: L 48 PHE cc_start: 0.6930 (t80) cc_final: 0.6670 (t80) REVERT: L 199 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: L 202 GLU cc_start: 0.8218 (tt0) cc_final: 0.7983 (tt0) REVERT: L 305 MET cc_start: 0.8356 (ttm) cc_final: 0.8126 (ttp) REVERT: Q 196 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7387 (mmpt) REVERT: Q 199 GLU cc_start: 0.7625 (pt0) cc_final: 0.7295 (pp20) REVERT: Q 231 GLU cc_start: 0.7156 (tp30) cc_final: 0.6619 (tp30) REVERT: Q 323 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7949 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7964 (mp10) outliers start: 34 outliers final: 14 residues processed: 210 average time/residue: 0.5010 time to fit residues: 112.4576 Evaluate side-chains 213 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.117323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097944 restraints weight = 15967.440| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.37 r_work: 0.2861 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.149 Angle : 0.558 7.206 12528 Z= 0.296 Chirality : 0.040 0.127 1491 Planarity : 0.004 0.041 1505 Dihedral : 7.328 104.751 1265 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.54 % Allowed : 13.20 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.34 (0.24), residues: 1143 helix: 2.24 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.12 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 154 TYR 0.020 0.002 TYR Q 244 PHE 0.015 0.002 PHE L 54 TRP 0.010 0.001 TRP K 16 HIS 0.004 0.001 HIS L 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 9199) covalent geometry : angle 0.55793 / 0.30 (12528) hydrogen bonds : bond 0.05685 / 3.74 ( 658) hydrogen bonds : angle 4.98600 / 3.68 ( 1933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.236 Fit side-chains REVERT: K 11 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6997 (mtt90) REVERT: K 16 TRP cc_start: 0.7514 (OUTLIER) cc_final: 0.5498 (t-100) REVERT: K 100 GLN cc_start: 0.5558 (OUTLIER) cc_final: 0.5094 (tp-100) REVERT: K 201 ARG cc_start: 0.8274 (mmt180) cc_final: 0.7898 (tpp-160) REVERT: K 329 HIS cc_start: 0.6295 (OUTLIER) cc_final: 0.5679 (m-70) REVERT: K 364 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6749 (mm) REVERT: K 379 THR cc_start: 0.8321 (m) cc_final: 0.8055 (t) REVERT: K 382 LEU cc_start: 0.8291 (mt) cc_final: 0.7881 (tp) REVERT: K 390 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7556 (mp) REVERT: L 48 PHE cc_start: 0.6847 (t80) cc_final: 0.6566 (t80) REVERT: L 199 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: L 202 GLU cc_start: 0.8248 (tt0) cc_final: 0.8022 (tt0) REVERT: L 305 MET cc_start: 0.8318 (ttm) cc_final: 0.8086 (ttp) REVERT: Q 196 LYS cc_start: 0.7852 (mmmm) cc_final: 0.7360 (mmpt) REVERT: Q 199 GLU cc_start: 0.7680 (pt0) cc_final: 0.7350 (pp20) REVERT: Q 231 GLU cc_start: 0.7163 (tp30) cc_final: 0.6710 (tp30) REVERT: Q 323 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7960 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: Q 407 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7910 (tppt) outliers start: 33 outliers final: 15 residues processed: 209 average time/residue: 0.4668 time to fit residues: 104.3326 Evaluate side-chains 217 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 49 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.114636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.094793 restraints weight = 19041.013| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.45 r_work: 0.2811 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9199 Z= 0.195 Angle : 0.621 8.399 12528 Z= 0.328 Chirality : 0.043 0.151 1491 Planarity : 0.005 0.041 1505 Dihedral : 7.499 104.335 1265 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.76 % Allowed : 13.20 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.24), residues: 1143 helix: 2.08 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.15 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 154 TYR 0.021 0.003 TYR Q 244 PHE 0.021 0.002 PHE L 54 TRP 0.010 0.002 TRP K 16 HIS 0.005 0.001 HIS Q 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 9199) covalent geometry : angle 0.62115 / 0.33 (12528) hydrogen bonds : bond 0.06451 / 4.25 ( 658) hydrogen bonds : angle 5.11287 / 3.77 ( 1933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.344 Fit side-chains REVERT: K 11 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7078 (mtt90) REVERT: K 100 GLN cc_start: 0.5598 (OUTLIER) cc_final: 0.5358 (tp-100) REVERT: K 329 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.5809 (m-70) REVERT: K 364 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6724 (mm) REVERT: K 382 LEU cc_start: 0.8318 (mt) cc_final: 0.7902 (tp) REVERT: K 390 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7604 (mp) REVERT: L 48 PHE cc_start: 0.6925 (t80) cc_final: 0.6698 (t80) REVERT: L 199 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: L 202 GLU cc_start: 0.8284 (tt0) cc_final: 0.8050 (tt0) REVERT: L 305 MET cc_start: 0.8374 (ttm) cc_final: 0.8139 (ttp) REVERT: Q 196 LYS cc_start: 0.7832 (mmmm) cc_final: 0.7350 (mmpt) REVERT: Q 199 GLU cc_start: 0.7705 (pt0) cc_final: 0.7359 (pp20) REVERT: Q 231 GLU cc_start: 0.7198 (tp30) cc_final: 0.6654 (tp30) REVERT: Q 323 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7970 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7978 (mp10) outliers start: 35 outliers final: 17 residues processed: 205 average time/residue: 0.4811 time to fit residues: 105.5380 Evaluate side-chains 214 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.114422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095181 restraints weight = 16027.849| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.36 r_work: 0.2806 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9199 Z= 0.201 Angle : 0.631 8.986 12528 Z= 0.333 Chirality : 0.043 0.142 1491 Planarity : 0.005 0.041 1505 Dihedral : 7.530 104.286 1265 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.54 % Allowed : 13.73 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.24), residues: 1143 helix: 2.02 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.18 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 154 TYR 0.021 0.003 TYR Q 244 PHE 0.021 0.002 PHE L 54 TRP 0.012 0.002 TRP K 220 HIS 0.005 0.001 HIS Q 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 9199) covalent geometry : angle 0.63104 / 0.33 (12528) hydrogen bonds : bond 0.06518 / 4.29 ( 658) hydrogen bonds : angle 5.13586 / 3.79 ( 1933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.320 Fit side-chains REVERT: K 11 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7059 (mtt90) REVERT: K 329 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5828 (m-70) REVERT: K 364 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6690 (mm) REVERT: K 382 LEU cc_start: 0.8310 (mt) cc_final: 0.7897 (tp) REVERT: K 390 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7620 (mp) REVERT: L 48 PHE cc_start: 0.6961 (t80) cc_final: 0.6729 (t80) REVERT: L 199 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: L 202 GLU cc_start: 0.8293 (tt0) cc_final: 0.8062 (tt0) REVERT: L 305 MET cc_start: 0.8374 (ttm) cc_final: 0.8143 (ttp) REVERT: Q 196 LYS cc_start: 0.7809 (mmmm) cc_final: 0.7328 (mmpt) REVERT: Q 199 GLU cc_start: 0.7715 (pt0) cc_final: 0.7363 (pp20) REVERT: Q 231 GLU cc_start: 0.7213 (tp30) cc_final: 0.6665 (tp30) REVERT: Q 323 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7971 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7979 (mp10) outliers start: 33 outliers final: 18 residues processed: 202 average time/residue: 0.4728 time to fit residues: 102.2076 Evaluate side-chains 212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN L 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.100662 restraints weight = 14238.236| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.29 r_work: 0.2906 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9199 Z= 0.133 Angle : 0.536 9.093 12528 Z= 0.283 Chirality : 0.038 0.126 1491 Planarity : 0.004 0.040 1505 Dihedral : 6.844 103.733 1262 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.90 % Allowed : 14.27 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.49 (0.24), residues: 1143 helix: 2.33 (0.17), residues: 815 sheet: None (None), residues: 0 loop : -0.10 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 154 TYR 0.018 0.002 TYR Q 244 PHE 0.016 0.002 PHE L 294 TRP 0.011 0.001 TRP K 220 HIS 0.005 0.001 HIS L 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9199) covalent geometry : angle 0.53624 / 0.28 (12528) hydrogen bonds : bond 0.05207 / 3.43 ( 658) hydrogen bonds : angle 4.91691 / 3.63 ( 1933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.284 Fit side-chains REVERT: K 11 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6983 (mtt90) REVERT: K 201 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7950 (tpp-160) REVERT: K 329 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5630 (m-70) REVERT: K 364 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6781 (mm) REVERT: K 379 THR cc_start: 0.8302 (m) cc_final: 0.8034 (t) REVERT: K 382 LEU cc_start: 0.8275 (mt) cc_final: 0.7753 (tp) REVERT: L 48 PHE cc_start: 0.6802 (t80) cc_final: 0.6116 (t80) REVERT: L 202 GLU cc_start: 0.8227 (tt0) cc_final: 0.8013 (tt0) REVERT: L 305 MET cc_start: 0.8210 (ttm) cc_final: 0.7984 (ttp) REVERT: Q 101 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7445 (mp) REVERT: Q 196 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7485 (mtmt) REVERT: Q 199 GLU cc_start: 0.7656 (pt0) cc_final: 0.7329 (pp20) REVERT: Q 231 GLU cc_start: 0.7120 (tp30) cc_final: 0.6676 (tp30) REVERT: Q 323 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: Q 407 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7897 (tppt) outliers start: 27 outliers final: 14 residues processed: 207 average time/residue: 0.4636 time to fit residues: 102.6263 Evaluate side-chains 214 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098559 restraints weight = 10120.824| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 0.93 r_work: 0.2883 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9199 Z= 0.178 Angle : 0.607 9.371 12528 Z= 0.320 Chirality : 0.042 0.143 1491 Planarity : 0.005 0.041 1505 Dihedral : 6.779 103.553 1257 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.68 % Allowed : 14.59 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.28 (0.24), residues: 1143 helix: 2.19 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.15 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 154 TYR 0.021 0.002 TYR Q 244 PHE 0.019 0.002 PHE L 54 TRP 0.020 0.002 TRP K 220 HIS 0.005 0.001 HIS Q 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 9199) covalent geometry : angle 0.60715 / 0.32 (12528) hydrogen bonds : bond 0.06171 / 4.06 ( 658) hydrogen bonds : angle 5.06249 / 3.73 ( 1933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.304 Fit side-chains REVERT: K 11 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6942 (mtt90) REVERT: K 201 ARG cc_start: 0.8305 (mmt180) cc_final: 0.7907 (tpp-160) REVERT: K 304 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8188 (mt) REVERT: K 329 HIS cc_start: 0.6311 (OUTLIER) cc_final: 0.5802 (m-70) REVERT: K 364 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6759 (mm) REVERT: K 379 THR cc_start: 0.8327 (m) cc_final: 0.8046 (t) REVERT: K 382 LEU cc_start: 0.8275 (mt) cc_final: 0.7874 (tp) REVERT: K 390 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7610 (mp) REVERT: L 48 PHE cc_start: 0.6867 (t80) cc_final: 0.6622 (t80) REVERT: L 202 GLU cc_start: 0.8142 (tt0) cc_final: 0.7890 (tt0) REVERT: L 305 MET cc_start: 0.8266 (ttm) cc_final: 0.8036 (ttp) REVERT: Q 196 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7511 (mtmt) REVERT: Q 199 GLU cc_start: 0.7519 (pt0) cc_final: 0.7227 (pp20) REVERT: Q 231 GLU cc_start: 0.7077 (tp30) cc_final: 0.6565 (tp30) REVERT: Q 323 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7889 (mtt-85) REVERT: Q 390 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7951 (mp10) outliers start: 25 outliers final: 12 residues processed: 201 average time/residue: 0.4703 time to fit residues: 101.1600 Evaluate side-chains 206 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 391 LYS Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 323 ARG Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 390 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098339 restraints weight = 14048.340| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.27 r_work: 0.2859 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9199 Z= 0.155 Angle : 0.575 9.360 12528 Z= 0.304 Chirality : 0.040 0.128 1491 Planarity : 0.004 0.040 1505 Dihedral : 6.694 103.330 1257 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.47 % Allowed : 15.02 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.24), residues: 1143 helix: 2.26 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -0.15 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 154 TYR 0.020 0.002 TYR Q 244 PHE 0.016 0.002 PHE L 294 TRP 0.020 0.002 TRP K 220 HIS 0.005 0.001 HIS L 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 9199) covalent geometry : angle 0.57450 / 0.30 (12528) hydrogen bonds : bond 0.05749 / 3.78 ( 658) hydrogen bonds : angle 5.00510 / 3.69 ( 1933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.90 seconds wall clock time: 59 minutes 24.25 seconds (3564.25 seconds total)