Starting phenix.real_space_refine on Thu Mar 5 07:59:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzq_26916/03_2026/7uzq_26916_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzq_26916/03_2026/7uzq_26916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uzq_26916/03_2026/7uzq_26916_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzq_26916/03_2026/7uzq_26916_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uzq_26916/03_2026/7uzq_26916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzq_26916/03_2026/7uzq_26916.map" } resolution = 2.17 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= 0.002 sd= 0.354 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 69 5.16 5 C 6690 2.51 5 N 1642 2.21 5 O 2002 1.98 5 H 10214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20617 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 6022 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 5958 Classifications: {'peptide': 380} Modifications used: {'COO': 1} 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, 5958 Classifications: {'peptide': 380} Modifications used: {'COO': 1} 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: 5959 Chain: "L" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 5916 Classifications: {'peptide': 388} Modifications used: {'COO': 1, 'NH3': 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: 5943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 5943 Classifications: {'peptide': 390} Modifications used: {'COO': 1, 'NH3': 1} 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: "J" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2370 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 224 Unresolved non-hydrogen chiralities: 43 Chain: "K" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "L" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "Q" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR K 34 " occ=0.55 ... (38 atoms not shown) pdb=" HH BTYR K 34 " occ=0.45 residue: pdb=" N APHE K 239 " occ=0.58 ... (38 atoms not shown) pdb=" HZ BPHE K 239 " occ=0.42 residue: pdb=" N ATYR K 242 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR K 242 " occ=0.47 Time building chain proxies: 4.41, per 1000 atoms: 0.21 Number of scatterers: 20617 At special positions: 0 Unit cell: (99.6, 92.96, 102.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 O 2002 8.00 N 1642 7.00 C 6690 6.00 H 10214 1.00 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: 1.76 Conformation dependent library (CDL) restraints added in 633.9 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 3 sheets defined 78.3% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'K' and resid 11 through 31 Processing helix chain 'K' and resid 43 through 60 removed outlier: 3.757A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 66 removed outlier: 3.769A pdb=" N THR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 removed outlier: 3.741A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 removed outlier: 3.544A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.577A 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 Processing helix chain 'K' and resid 171 through 187 Processing helix chain 'K' and resid 202 through 220 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 230 through 257 removed outlier: 4.442A pdb=" N SER K 257 " --> pdb=" O ILE K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 274 removed outlier: 3.644A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 290 through 312 removed outlier: 3.629A pdb=" N ALA K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 348 removed outlier: 3.626A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 389 Processing helix chain 'K' and resid 390 through 394 removed outlier: 3.509A pdb=" N TRP K 393 " --> pdb=" O LEU K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.606A 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 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 75 through 104 removed outlier: 3.653A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 133 removed outlier: 3.681A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 162 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: 3.648A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.758A 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 262 removed outlier: 3.637A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 266 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.626A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 321 removed outlier: 3.502A pdb=" N GLY L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 4.381A 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 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 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: 3.829A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 133 removed outlier: 3.736A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 162 removed outlier: 3.607A 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: 3.586A 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 291 through 321 removed outlier: 3.627A pdb=" N GLY Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) removed outlier: 4.358A 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 334 through 351 Processing helix chain 'Q' and resid 357 through 385 removed outlier: 3.804A pdb=" N LEU Q 385 " --> pdb=" O LEU Q 381 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 396 Processing helix chain 'Q' and resid 398 through 402 Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 24 through 34 Processing helix chain 'J' and resid 47 through 56 Processing helix chain 'J' and resid 57 through 67 Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 90 through 100 Processing helix chain 'J' and resid 113 through 121 Processing helix chain 'J' and resid 123 through 133 Processing helix chain 'J' and resid 146 through 154 Processing helix chain 'J' and resid 156 through 167 Processing sheet with id=AA1, first strand: chain 'K' and resid 32 through 33 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 25 734 hydrogen bonds defined for protein. 2151 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: 4.27 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10198 1.03 - 1.23: 273 1.23 - 1.43: 4061 1.43 - 1.62: 5979 1.62 - 1.82: 122 Bond restraints: 20633 Sorted by residual: bond pdb=" C ALA Q 364 " pdb=" O ALA Q 364 " ideal model delta sigma weight residual 1.236 1.170 0.067 1.15e-02 7.56e+03 3.35e+01 bond pdb=" C ALA Q 287 " pdb=" O ALA Q 287 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.88e+01 bond pdb=" C SER Q 171 " pdb=" O SER Q 171 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.16e-02 7.43e+03 1.64e+01 bond pdb=" C MET Q 8 " pdb=" O MET Q 8 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.19e-02 7.06e+03 1.63e+01 bond pdb=" C ASP K 404 " pdb=" O ASP K 404 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.25e-02 6.40e+03 1.43e+01 ... (remaining 20628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 36470 2.34 - 4.67: 769 4.67 - 7.01: 40 7.01 - 9.34: 2 9.34 - 11.68: 1 Bond angle restraints: 37282 Sorted by residual: angle pdb=" N MET Q 172 " pdb=" CA MET Q 172 " pdb=" C MET Q 172 " ideal model delta sigma weight residual 111.36 118.76 -7.40 1.09e+00 8.42e-01 4.61e+01 angle pdb=" CA HIS J 123 " pdb=" C HIS J 123 " pdb=" O HIS J 123 " ideal model delta sigma weight residual 122.37 116.80 5.57 1.15e+00 7.56e-01 2.34e+01 angle pdb=" N ALA Q 353 " pdb=" CA ALA Q 353 " pdb=" C ALA Q 353 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N SER Q 171 " pdb=" CA SER Q 171 " pdb=" C SER Q 171 " ideal model delta sigma weight residual 111.02 105.23 5.79 1.22e+00 6.72e-01 2.25e+01 angle pdb=" CA VAL K 406 " pdb=" C VAL K 406 " pdb=" O VAL K 406 " ideal model delta sigma weight residual 120.95 116.60 4.35 1.04e+00 9.25e-01 1.75e+01 ... (remaining 37277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 9214 24.22 - 48.45: 522 48.45 - 72.67: 211 72.67 - 96.90: 23 96.90 - 121.12: 9 Dihedral angle restraints: 9979 sinusoidal: 5409 harmonic: 4570 Sorted by residual: 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 63.52 -121.12 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" O34 AJP Q 502 " pdb=" C28 AJP Q 502 " pdb=" C29 AJP Q 502 " pdb=" O77 AJP Q 502 " ideal model delta sinusoidal sigma weight residual -58.96 61.69 -120.65 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA TRP L 403 " pdb=" C TRP L 403 " pdb=" N LYS L 404 " pdb=" CA LYS L 404 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 9976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1305 0.055 - 0.111: 306 0.111 - 0.166: 58 0.166 - 0.222: 10 0.222 - 0.277: 5 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA VAL K 249 " pdb=" N VAL K 249 " pdb=" C VAL K 249 " pdb=" CB VAL K 249 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.92e+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 2.48 -0.28 2.00e-01 2.50e+01 1.91e+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 2.81 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1681 not shown) Planarity restraints: 2996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 361 " 0.248 2.00e-02 2.50e+03 3.06e-01 1.40e+03 pdb=" CD GLN Q 361 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 361 " -0.242 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 361 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN Q 361 " -0.464 2.00e-02 2.50e+03 pdb="HE22 GLN Q 361 " 0.475 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 120 " -0.094 2.00e-02 2.50e+03 9.67e-02 1.40e+02 pdb=" CD GLN J 120 " 0.012 2.00e-02 2.50e+03 pdb=" OE1 GLN J 120 " 0.085 2.00e-02 2.50e+03 pdb=" NE2 GLN J 120 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN J 120 " 0.139 2.00e-02 2.50e+03 pdb="HE22 GLN J 120 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 405 " -0.062 2.00e-02 2.50e+03 6.53e-02 6.40e+01 pdb=" CD GLN K 405 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN K 405 " 0.060 2.00e-02 2.50e+03 pdb=" NE2 GLN K 405 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN K 405 " 0.095 2.00e-02 2.50e+03 pdb="HE22 GLN K 405 " -0.096 2.00e-02 2.50e+03 ... (remaining 2993 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 2585 2.25 - 2.84: 46961 2.84 - 3.43: 62306 3.43 - 4.01: 84873 4.01 - 4.60: 128279 Nonbonded interactions: 325004 Sorted by model distance: nonbonded pdb=" O PHE L 67 " pdb=" HG1 THR L 70 " model vdw 1.667 2.450 nonbonded pdb=" H VAL L 405 " pdb=" O HOH L 615 " model vdw 1.697 2.450 nonbonded pdb=" O PHE K 28 " pdb=" HG1 THR K 32 " model vdw 1.702 2.450 nonbonded pdb="HH22 ARG K 154 " pdb=" O HOH K 502 " model vdw 1.706 2.450 nonbonded pdb=" HE ARG L 264 " pdb=" O HOH K 503 " model vdw 1.708 2.450 ... (remaining 324999 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 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1 or name HE2 or name HZ )) or resid 49 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=0.42 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: 1.130 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: 0.130 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.220 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 0.088 10419 Z= 0.399 Angle : 0.922 7.403 14183 Z= 0.608 Chirality : 0.051 0.277 1684 Planarity : 0.006 0.094 1726 Dihedral : 17.122 121.121 3876 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % Rotamer: Outliers : 2.27 % Allowed : 12.95 % Favored : 84.78 % 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: 2.16 (0.23), residues: 1301 helix: 1.94 (0.17), residues: 923 sheet: None (None), residues: 0 loop : 0.27 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 195 TYR 0.042 0.003 TYR Q 180 PHE 0.020 0.003 PHE L 245 TRP 0.017 0.002 TRP K 220 HIS 0.011 0.002 HIS J 162 Details of bonding type rmsd covalent geometry : bond 0.00629 (10419) covalent geometry : angle 0.92240 (14183) hydrogen bonds : bond 0.13012 ( 734) hydrogen bonds : angle 5.77796 ( 2151) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.467 Fit side-chains REVERT: K 329 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.6166 (t-90) outliers start: 23 outliers final: 15 residues processed: 196 average time/residue: 1.1475 time to fit residues: 244.0967 Evaluate side-chains 190 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 333 SER Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 237 CYS Chi-restraints excluded: chain Q residue 294 PHE Chi-restraints excluded: chain Q residue 349 VAL Chi-restraints excluded: chain J residue 71 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN L 58 HIS Q 104 GLN ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.124078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.096396 restraints weight = 35915.790| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.07 r_work: 0.2836 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10419 Z= 0.145 Angle : 0.551 6.517 14183 Z= 0.301 Chirality : 0.037 0.130 1684 Planarity : 0.004 0.055 1726 Dihedral : 7.066 59.809 1755 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.47 % Favored : 98.45 % Rotamer: Outliers : 2.65 % Allowed : 12.76 % Favored : 84.59 % 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: 2.46 (0.23), residues: 1301 helix: 2.21 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.19 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 195 TYR 0.022 0.002 TYR Q 180 PHE 0.017 0.002 PHE K 172 TRP 0.008 0.001 TRP K 185 HIS 0.004 0.001 HIS L 154 Details of bonding type rmsd covalent geometry : bond 0.00276 (10419) covalent geometry : angle 0.55115 (14183) hydrogen bonds : bond 0.06091 ( 734) hydrogen bonds : angle 4.94366 ( 2151) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.575 Fit side-chains REVERT: K 340 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: L 231 GLU cc_start: 0.7865 (tt0) cc_final: 0.7662 (mt-10) outliers start: 27 outliers final: 14 residues processed: 193 average time/residue: 1.1380 time to fit residues: 238.6268 Evaluate side-chains 188 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 230 SER Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 333 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS ** J 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.093871 restraints weight = 40151.838| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.14 r_work: 0.2801 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10419 Z= 0.159 Angle : 0.554 4.724 14183 Z= 0.307 Chirality : 0.037 0.129 1684 Planarity : 0.004 0.053 1726 Dihedral : 6.066 57.224 1744 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.70 % Favored : 98.22 % Rotamer: Outliers : 2.36 % Allowed : 13.33 % Favored : 84.31 % 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 (0.23), residues: 1301 helix: 2.17 (0.17), residues: 924 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 409 TYR 0.024 0.002 TYR Q 180 PHE 0.018 0.002 PHE L 54 TRP 0.009 0.001 TRP K 185 HIS 0.005 0.001 HIS L 154 Details of bonding type rmsd covalent geometry : bond 0.00308 (10419) covalent geometry : angle 0.55404 (14183) hydrogen bonds : bond 0.06383 ( 734) hydrogen bonds : angle 4.94828 ( 2151) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.549 Fit side-chains REVERT: K 16 TRP cc_start: 0.7496 (OUTLIER) cc_final: 0.6418 (t-100) REVERT: K 340 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: L 231 GLU cc_start: 0.7873 (tt0) cc_final: 0.7604 (mt-10) outliers start: 24 outliers final: 11 residues processed: 187 average time/residue: 1.1363 time to fit residues: 230.5185 Evaluate side-chains 188 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 230 SER Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS J 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.092264 restraints weight = 35850.525| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.07 r_work: 0.2777 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 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 = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10419 Z= 0.206 Angle : 0.612 5.124 14183 Z= 0.339 Chirality : 0.040 0.127 1684 Planarity : 0.005 0.054 1726 Dihedral : 6.154 56.638 1741 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.76 % Rotamer: Outliers : 2.84 % Allowed : 12.95 % Favored : 84.22 % 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: 2.09 (0.23), residues: 1301 helix: 1.96 (0.17), residues: 924 sheet: None (None), residues: 0 loop : 0.01 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 71 TYR 0.027 0.003 TYR Q 180 PHE 0.023 0.002 PHE L 245 TRP 0.011 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 Details of bonding type rmsd covalent geometry : bond 0.00416 (10419) covalent geometry : angle 0.61178 (14183) hydrogen bonds : bond 0.07088 ( 734) hydrogen bonds : angle 5.10208 ( 2151) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: L 231 GLU cc_start: 0.7862 (tt0) cc_final: 0.7660 (mt-10) REVERT: Q 1 MET cc_start: 0.5768 (OUTLIER) cc_final: 0.4745 (pmm) REVERT: Q 351 MET cc_start: 0.8011 (mmp) cc_final: 0.7800 (mmt) outliers start: 29 outliers final: 17 residues processed: 188 average time/residue: 1.1137 time to fit residues: 227.0295 Evaluate side-chains 186 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 269 MET Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 50.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 233 GLN K 236 ASN L 58 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.093335 restraints weight = 36109.125| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.07 r_work: 0.2789 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10419 Z= 0.179 Angle : 0.576 5.051 14183 Z= 0.320 Chirality : 0.038 0.128 1684 Planarity : 0.004 0.053 1726 Dihedral : 5.949 57.593 1741 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 2.17 % Allowed : 13.23 % Favored : 84.59 % 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: 2.13 (0.23), residues: 1301 helix: 2.01 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.02 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 71 TYR 0.024 0.002 TYR Q 180 PHE 0.021 0.002 PHE Q 257 TRP 0.012 0.002 TRP K 185 HIS 0.006 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00353 (10419) covalent geometry : angle 0.57589 (14183) hydrogen bonds : bond 0.06646 ( 734) hydrogen bonds : angle 5.01140 ( 2151) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.537 Fit side-chains REVERT: K 16 TRP cc_start: 0.7507 (OUTLIER) cc_final: 0.6414 (t-100) REVERT: K 340 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6036 (mp0) outliers start: 22 outliers final: 13 residues processed: 183 average time/residue: 1.1300 time to fit residues: 225.1638 Evaluate side-chains 184 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 269 MET Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 0.0000 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.094628 restraints weight = 38364.774| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.11 r_work: 0.2812 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10419 Z= 0.151 Angle : 0.539 5.080 14183 Z= 0.298 Chirality : 0.037 0.130 1684 Planarity : 0.004 0.053 1726 Dihedral : 5.679 58.346 1735 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 1.61 % Allowed : 13.99 % Favored : 84.40 % 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 (0.23), residues: 1301 helix: 2.19 (0.17), residues: 918 sheet: None (None), residues: 0 loop : 0.02 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 409 TYR 0.020 0.002 TYR Q 180 PHE 0.019 0.002 PHE Q 257 TRP 0.011 0.001 TRP K 185 HIS 0.007 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00290 (10419) covalent geometry : angle 0.53855 (14183) hydrogen bonds : bond 0.06111 ( 734) hydrogen bonds : angle 4.89572 ( 2151) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.561 Fit side-chains REVERT: K 16 TRP cc_start: 0.7449 (OUTLIER) cc_final: 0.6401 (t-100) REVERT: K 340 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.5987 (mp0) outliers start: 16 outliers final: 9 residues processed: 179 average time/residue: 1.2114 time to fit residues: 235.0396 Evaluate side-chains 181 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 66 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 6.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.091911 restraints weight = 35241.178| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.06 r_work: 0.2774 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10419 Z= 0.220 Angle : 0.627 5.445 14183 Z= 0.348 Chirality : 0.041 0.125 1684 Planarity : 0.005 0.054 1726 Dihedral : 6.097 59.135 1735 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.76 % Rotamer: Outliers : 2.27 % Allowed : 13.71 % Favored : 84.03 % 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: 1.98 (0.23), residues: 1301 helix: 1.88 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.04 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 191 TYR 0.027 0.003 TYR Q 180 PHE 0.025 0.002 PHE L 245 TRP 0.014 0.002 TRP K 185 HIS 0.006 0.002 HIS L 154 Details of bonding type rmsd covalent geometry : bond 0.00451 (10419) covalent geometry : angle 0.62672 (14183) hydrogen bonds : bond 0.07254 ( 734) hydrogen bonds : angle 5.13906 ( 2151) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6005 (mp0) REVERT: Q 1 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5008 (pmm) outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 1.1843 time to fit residues: 234.2270 Evaluate side-chains 184 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS L 394 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.092572 restraints weight = 36778.126| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.08 r_work: 0.2781 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10419 Z= 0.197 Angle : 0.599 5.241 14183 Z= 0.333 Chirality : 0.039 0.127 1684 Planarity : 0.005 0.054 1726 Dihedral : 5.996 58.169 1735 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.76 % Rotamer: Outliers : 2.17 % Allowed : 13.71 % Favored : 84.12 % 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: 1.97 (0.23), residues: 1301 helix: 1.89 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -0.08 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 71 TYR 0.025 0.003 TYR Q 180 PHE 0.022 0.002 PHE Q 257 TRP 0.014 0.002 TRP K 185 HIS 0.007 0.002 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00397 (10419) covalent geometry : angle 0.59895 (14183) hydrogen bonds : bond 0.06910 ( 734) hydrogen bonds : angle 5.07416 ( 2151) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 340 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.5990 (mp0) outliers start: 22 outliers final: 15 residues processed: 178 average time/residue: 1.1721 time to fit residues: 225.9081 Evaluate side-chains 182 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.092498 restraints weight = 41129.608| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.14 r_work: 0.2776 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10419 Z= 0.185 Angle : 0.588 5.850 14183 Z= 0.326 Chirality : 0.039 0.128 1684 Planarity : 0.004 0.054 1726 Dihedral : 5.939 56.904 1735 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 1.98 % Allowed : 13.80 % Favored : 84.22 % 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 (0.23), residues: 1301 helix: 1.94 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.08 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 71 TYR 0.023 0.002 TYR Q 180 PHE 0.022 0.002 PHE Q 257 TRP 0.014 0.002 TRP K 185 HIS 0.008 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00370 (10419) covalent geometry : angle 0.58805 (14183) hydrogen bonds : bond 0.06743 ( 734) hydrogen bonds : angle 5.03466 ( 2151) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: K 334 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7308 (tt) REVERT: K 340 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6006 (mp0) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 1.1989 time to fit residues: 230.9140 Evaluate side-chains 182 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 334 LEU Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.094946 restraints weight = 37463.135| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.09 r_work: 0.2816 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10419 Z= 0.152 Angle : 0.550 6.322 14183 Z= 0.304 Chirality : 0.037 0.131 1684 Planarity : 0.004 0.054 1726 Dihedral : 5.565 56.455 1731 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 1.51 % Allowed : 14.46 % Favored : 84.03 % 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: 2.25 (0.23), residues: 1301 helix: 2.15 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -0.07 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 409 TYR 0.019 0.002 TYR Q 180 PHE 0.018 0.002 PHE Q 257 TRP 0.012 0.001 TRP K 185 HIS 0.009 0.001 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00298 (10419) covalent geometry : angle 0.55000 (14183) hydrogen bonds : bond 0.06109 ( 734) hydrogen bonds : angle 4.89747 ( 2151) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.552 Fit side-chains REVERT: K 16 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6395 (t-100) REVERT: K 340 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.5968 (mp0) outliers start: 15 outliers final: 9 residues processed: 178 average time/residue: 1.2054 time to fit residues: 232.9942 Evaluate side-chains 179 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN K 236 ASN L 58 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.120047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.092023 restraints weight = 35893.415| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.07 r_work: 0.2771 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10419 Z= 0.222 Angle : 0.628 5.806 14183 Z= 0.348 Chirality : 0.041 0.125 1684 Planarity : 0.005 0.055 1726 Dihedral : 5.897 54.703 1731 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.09 % Favored : 97.83 % Rotamer: Outliers : 1.70 % Allowed : 14.56 % Favored : 83.74 % 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: 1.95 (0.23), residues: 1301 helix: 1.88 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -0.10 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 191 TYR 0.027 0.003 TYR Q 180 PHE 0.024 0.003 PHE L 245 TRP 0.015 0.002 TRP K 185 HIS 0.008 0.002 HIS Q 263 Details of bonding type rmsd covalent geometry : bond 0.00457 (10419) covalent geometry : angle 0.62789 (14183) hydrogen bonds : bond 0.07197 ( 734) hydrogen bonds : angle 5.11529 ( 2151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8550.99 seconds wall clock time: 145 minutes 13.03 seconds (8713.03 seconds total)