Starting phenix.real_space_refine on Sat Jan 18 03:13:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzx_18784/01_2025/8qzx_18784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzx_18784/01_2025/8qzx_18784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qzx_18784/01_2025/8qzx_18784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzx_18784/01_2025/8qzx_18784.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzx_18784/01_2025/8qzx_18784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzx_18784/01_2025/8qzx_18784.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 7471 2.51 5 N 1965 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11708 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2620 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 317} Chain breaks: 2 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2618 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2629 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2580 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Chain breaks: 3 Chain: "E" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1055 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1B NAD A 401 " occ=0.73 ... (42 atoms not shown) pdb=" PN NAD A 401 " occ=0.73 residue: pdb=" C1B NAD B 401 " occ=0.88 ... (42 atoms not shown) pdb=" PN NAD B 401 " occ=0.88 residue: pdb=" C1B NAD C 401 " occ=0.75 ... (42 atoms not shown) pdb=" PN NAD C 401 " occ=0.75 residue: pdb=" C1B NAD D 402 " occ=0.79 ... (42 atoms not shown) pdb=" PN NAD D 402 " occ=0.79 Time building chain proxies: 7.53, per 1000 atoms: 0.64 Number of scatterers: 11708 At special positions: 0 Unit cell: (79.4864, 96.3984, 145.443, 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 68 16.00 P 8 15.00 O 2196 8.00 N 1965 7.00 C 7471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 53.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.868A pdb=" N ASN A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.573A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.796A pdb=" N PHE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 174 through 200 removed outlier: 4.089A pdb=" N TYR A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 204 through 217 removed outlier: 4.008A pdb=" N ASN A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 removed outlier: 3.576A pdb=" N TRP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.530A pdb=" N ASP A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.243A pdb=" N ASP A 315 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.720A pdb=" N ALA A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.538A pdb=" N VAL A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.623A pdb=" N GLN B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 51 through 69 removed outlier: 3.639A pdb=" N ASN B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.907A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.532A pdb=" N HIS B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.827A pdb=" N PHE B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 175 through 200 removed outlier: 3.972A pdb=" N CYS B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Proline residue: B 187 - end of helix Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.762A pdb=" N ASN B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.627A pdb=" N TRP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 254 removed outlier: 3.703A pdb=" N TYR B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 312 through 316 removed outlier: 4.404A pdb=" N ASP B 315 " --> pdb=" O HIS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 removed outlier: 3.571A pdb=" N ALA B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 48 through 51 removed outlier: 4.560A pdb=" N GLY C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.821A pdb=" N ASN C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 removed outlier: 4.017A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.614A pdb=" N LEU C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.709A pdb=" N PHE C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 163 Processing helix chain 'C' and resid 174 through 200 removed outlier: 4.122A pdb=" N TYR C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 204 through 215 Processing helix chain 'C' and resid 221 through 229 removed outlier: 3.657A pdb=" N TRP C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 254 removed outlier: 3.607A pdb=" N ASP C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.795A pdb=" N ASP C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.569A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 4.018A pdb=" N ASP C 315 " --> pdb=" O HIS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.608A pdb=" N ALA C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.702A pdb=" N VAL C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.671A pdb=" N ASN D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 4.109A pdb=" N ILE D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 133 through 146 removed outlier: 3.738A pdb=" N PHE D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 175 through 200 removed outlier: 4.099A pdb=" N CYS D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Proline residue: D 187 - end of helix Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 241 through 252 removed outlier: 3.686A pdb=" N TYR D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.939A pdb=" N ASP D 264 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.926A pdb=" N TYR D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 removed outlier: 4.251A pdb=" N ASP D 315 " --> pdb=" O HIS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 removed outlier: 3.784A pdb=" N ALA D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 356 through 363 removed outlier: 3.541A pdb=" N PHE D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234 removed outlier: 7.047A pdb=" N VAL A 130 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 304 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 305 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL A 341 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 307 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.553A pdb=" N ILE B 101 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 131 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 103 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 305 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 341 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR B 307 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.574A pdb=" N ASN B 166 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 233 through 234 removed outlier: 7.059A pdb=" N VAL C 130 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'D' and resid 233 through 234 removed outlier: 6.877A pdb=" N VAL D 130 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL D 129 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 101 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL D 131 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 103 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 305 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL D 341 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR D 307 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.241A pdb=" N VAL E 47 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR E 68 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 92 removed outlier: 6.664A pdb=" N GLN E 107 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.724A pdb=" N ASP E 161 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU E 151 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 159 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER E 153 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1494 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: 4.66 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.19: 7 1.19 - 1.37: 3991 1.37 - 1.55: 7832 1.55 - 1.72: 51 1.72 - 1.90: 105 Bond restraints: 11986 Sorted by residual: bond pdb=" C ILE E 159 " pdb=" N VAL E 160 " ideal model delta sigma weight residual 1.335 1.015 0.320 1.22e-02 6.72e+03 6.89e+02 bond pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 1.331 1.022 0.308 1.41e-02 5.03e+03 4.78e+02 bond pdb=" C VAL E 146 " pdb=" N VAL E 147 " ideal model delta sigma weight residual 1.330 1.021 0.309 1.48e-02 4.57e+03 4.37e+02 bond pdb=" C TYR E 37 " pdb=" O TYR E 37 " ideal model delta sigma weight residual 1.234 1.475 -0.241 1.25e-02 6.40e+03 3.72e+02 bond pdb=" C ASP E 134 " pdb=" N LEU E 135 " ideal model delta sigma weight residual 1.333 1.049 0.284 1.55e-02 4.16e+03 3.36e+02 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.09: 16201 8.09 - 16.18: 56 16.18 - 24.27: 5 24.27 - 32.36: 3 32.36 - 40.45: 1 Bond angle restraints: 16266 Sorted by residual: angle pdb=" C GLY E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta sigma weight residual 121.85 162.30 -40.45 1.77e+00 3.19e-01 5.22e+02 angle pdb=" C ASN E 143 " pdb=" N ASP E 144 " pdb=" CA ASP E 144 " ideal model delta sigma weight residual 121.50 150.36 -28.86 1.43e+00 4.89e-01 4.07e+02 angle pdb=" O ASN E 143 " pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 122.39 95.96 26.43 1.48e+00 4.57e-01 3.19e+02 angle pdb=" CA TYR E 37 " pdb=" C TYR E 37 " pdb=" O TYR E 37 " ideal model delta sigma weight residual 121.66 100.37 21.29 1.22e+00 6.72e-01 3.05e+02 angle pdb=" CA ASN E 143 " pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 118.44 142.98 -24.54 1.41e+00 5.03e-01 3.03e+02 ... (remaining 16261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.08: 6395 19.08 - 38.16: 571 38.16 - 57.25: 141 57.25 - 76.33: 44 76.33 - 95.41: 22 Dihedral angle restraints: 7173 sinusoidal: 3002 harmonic: 4171 Sorted by residual: dihedral pdb=" CA GLY E 104 " pdb=" C GLY E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta harmonic sigma weight residual 180.00 122.21 57.79 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" C PHE D 52 " pdb=" N PHE D 52 " pdb=" CA PHE D 52 " pdb=" CB PHE D 52 " ideal model delta harmonic sigma weight residual -122.60 -138.72 16.12 0 2.50e+00 1.60e-01 4.16e+01 dihedral pdb=" C ASP D 303 " pdb=" N ASP D 303 " pdb=" CA ASP D 303 " pdb=" CB ASP D 303 " ideal model delta harmonic sigma weight residual -122.60 -135.59 12.99 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 7170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1058 0.110 - 0.219: 591 0.219 - 0.329: 124 0.329 - 0.439: 9 0.439 - 0.548: 3 Chirality restraints: 1785 Sorted by residual: chirality pdb=" CA PHE D 52 " pdb=" N PHE D 52 " pdb=" C PHE D 52 " pdb=" CB PHE D 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.52e+00 chirality pdb=" CA GLN E 130 " pdb=" N GLN E 130 " pdb=" C GLN E 130 " pdb=" CB GLN E 130 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 1782 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 401 " -0.096 2.00e-02 2.50e+03 7.76e-02 1.20e+02 pdb=" C2N NAD C 401 " 0.170 2.00e-02 2.50e+03 pdb=" C3N NAD C 401 " 0.020 2.00e-02 2.50e+03 pdb=" C4N NAD C 401 " -0.030 2.00e-02 2.50e+03 pdb=" C5N NAD C 401 " 0.017 2.00e-02 2.50e+03 pdb=" C6N NAD C 401 " -0.017 2.00e-02 2.50e+03 pdb=" C7N NAD C 401 " -0.087 2.00e-02 2.50e+03 pdb=" N1N NAD C 401 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 401 " 0.081 2.00e-02 2.50e+03 6.79e-02 9.23e+01 pdb=" C2N NAD A 401 " -0.018 2.00e-02 2.50e+03 pdb=" C3N NAD A 401 " 0.014 2.00e-02 2.50e+03 pdb=" C4N NAD A 401 " 0.111 2.00e-02 2.50e+03 pdb=" C5N NAD A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C6N NAD A 401 " -0.120 2.00e-02 2.50e+03 pdb=" C7N NAD A 401 " -0.049 2.00e-02 2.50e+03 pdb=" N1N NAD A 401 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 402 " 0.107 2.00e-02 2.50e+03 6.71e-02 9.01e+01 pdb=" C2N NAD D 402 " -0.112 2.00e-02 2.50e+03 pdb=" C3N NAD D 402 " 0.002 2.00e-02 2.50e+03 pdb=" C4N NAD D 402 " 0.083 2.00e-02 2.50e+03 pdb=" C5N NAD D 402 " -0.007 2.00e-02 2.50e+03 pdb=" C6N NAD D 402 " -0.060 2.00e-02 2.50e+03 pdb=" C7N NAD D 402 " 0.021 2.00e-02 2.50e+03 pdb=" N1N NAD D 402 " -0.034 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4405 2.90 - 3.40: 11287 3.40 - 3.90: 20052 3.90 - 4.40: 24306 4.40 - 4.90: 38363 Nonbonded interactions: 98413 Sorted by model distance: nonbonded pdb=" O ASP E 134 " pdb=" CA LEU E 135 " model vdw 2.405 2.776 nonbonded pdb=" O ALA D 226 " pdb=" N ILE D 231 " model vdw 2.408 3.120 nonbonded pdb=" N PHE E 136 " pdb=" N ASN E 137 " model vdw 2.420 2.560 nonbonded pdb=" O VAL E 146 " pdb=" CA VAL E 147 " model vdw 2.438 2.776 nonbonded pdb=" O ILE E 159 " pdb=" CA VAL E 160 " model vdw 2.453 2.776 ... (remaining 98408 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 'A' and (resid 26 through 34 or resid 38 through 73 or resid 81 through 1 \ 50 or resid 154 through 363)) selection = (chain 'B' and (resid 26 through 34 or resid 38 through 150 or resid 154 through \ 168 or resid 171 through 363)) selection = (chain 'C' and (resid 26 through 34 or resid 38 through 73 or resid 81 through 1 \ 50 or resid 154 through 168 or resid 171 through 363)) selection = (chain 'D' and (resid 26 through 73 or resid 81 through 168 or resid 171 through \ 363)) } 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=0.73 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.470 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.150 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: 0.030 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.320 11986 Z= 0.961 Angle : 1.923 40.445 16266 Z= 1.437 Chirality : 0.128 0.548 1785 Planarity : 0.008 0.078 2070 Dihedral : 16.904 95.409 4513 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 7.06 % Allowed : 12.51 % Favored : 80.43 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1440 helix: 1.62 (0.19), residues: 664 sheet: 0.57 (0.40), residues: 156 loop : -0.21 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 329 HIS 0.006 0.002 HIS B 250 PHE 0.032 0.003 PHE E 136 TYR 0.030 0.003 TYR C 70 ARG 0.009 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 273 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7447 (tpt) cc_final: 0.7169 (tpt) REVERT: A 150 MET cc_start: 0.6676 (mtp) cc_final: 0.5670 (mmt) REVERT: A 155 HIS cc_start: 0.4025 (OUTLIER) cc_final: 0.2898 (m90) REVERT: A 166 ASN cc_start: 0.7661 (t0) cc_final: 0.6897 (t0) REVERT: A 220 ASP cc_start: 0.5449 (t0) cc_final: 0.5193 (t0) REVERT: A 298 TYR cc_start: 0.7939 (m-80) cc_final: 0.7698 (m-10) REVERT: B 47 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6597 (mmt) REVERT: B 67 MET cc_start: 0.6728 (mtt) cc_final: 0.6436 (mtm) REVERT: B 130 VAL cc_start: 0.5044 (OUTLIER) cc_final: 0.4827 (t) REVERT: B 138 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: B 145 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7094 (mt) REVERT: B 278 THR cc_start: 0.7760 (p) cc_final: 0.7560 (p) REVERT: B 299 ARG cc_start: 0.5600 (ptp-110) cc_final: 0.5315 (tpt170) REVERT: B 329 TRP cc_start: 0.6341 (OUTLIER) cc_final: 0.5625 (m-10) REVERT: C 313 ASP cc_start: 0.6943 (p0) cc_final: 0.6569 (t0) REVERT: D 41 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6783 (t0) REVERT: D 73 GLU cc_start: 0.7044 (mp0) cc_final: 0.6391 (tm-30) REVERT: D 109 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6162 (mp) REVERT: D 163 ARG cc_start: 0.6646 (mtt180) cc_final: 0.6143 (mmt90) REVERT: D 176 LYS cc_start: 0.7309 (tttt) cc_final: 0.6633 (tptt) REVERT: D 361 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6238 (mp) outliers start: 88 outliers final: 15 residues processed: 345 average time/residue: 0.2371 time to fit residues: 119.7721 Evaluate side-chains 196 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 329 TRP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 361 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 108 ASN A 166 ASN A 296 ASN B 177 ASN B 230 ASN B 296 ASN C 46 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 46 GLN D 124 HIS E 84 HIS E 105 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.202707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.178958 restraints weight = 14838.101| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.88 r_work: 0.4087 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11986 Z= 0.237 Angle : 0.656 9.803 16266 Z= 0.348 Chirality : 0.046 0.160 1785 Planarity : 0.005 0.069 2070 Dihedral : 13.244 85.974 1849 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.13 % Allowed : 15.48 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1440 helix: 1.05 (0.19), residues: 694 sheet: 0.46 (0.37), residues: 188 loop : -0.14 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 203 HIS 0.006 0.001 HIS D 124 PHE 0.023 0.002 PHE A 357 TYR 0.020 0.002 TYR A 224 ARG 0.003 0.001 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6311 (mtp) cc_final: 0.5459 (mmt) REVERT: A 155 HIS cc_start: 0.4188 (OUTLIER) cc_final: 0.3746 (m90) REVERT: B 47 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.4740 (mpt) REVERT: B 299 ARG cc_start: 0.5649 (ptp-110) cc_final: 0.4896 (tpt170) REVERT: B 328 SER cc_start: 0.7516 (t) cc_final: 0.7215 (p) REVERT: B 344 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5998 (tt0) REVERT: C 260 ASP cc_start: 0.7601 (t0) cc_final: 0.7386 (t70) REVERT: C 313 ASP cc_start: 0.7600 (p0) cc_final: 0.6496 (t0) REVERT: D 41 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7147 (t0) REVERT: D 145 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7320 (mt) REVERT: D 176 LYS cc_start: 0.7122 (tttt) cc_final: 0.6677 (tptp) REVERT: D 186 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7369 (mtt) REVERT: D 359 LYS cc_start: 0.5542 (mptt) cc_final: 0.4340 (ptmt) outliers start: 39 outliers final: 21 residues processed: 228 average time/residue: 0.2618 time to fit residues: 84.6534 Evaluate side-chains 192 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 291 HIS B 108 ASN B 124 HIS B 269 ASN B 296 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.195885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168122 restraints weight = 15425.644| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.02 r_work: 0.3998 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11986 Z= 0.327 Angle : 0.668 7.745 16266 Z= 0.354 Chirality : 0.048 0.165 1785 Planarity : 0.005 0.066 2070 Dihedral : 11.904 73.592 1827 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.61 % Allowed : 16.60 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1440 helix: 0.49 (0.19), residues: 697 sheet: 0.21 (0.37), residues: 188 loop : -0.21 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 329 HIS 0.007 0.002 HIS D 124 PHE 0.020 0.002 PHE A 357 TYR 0.020 0.002 TYR A 224 ARG 0.008 0.001 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 153 PHE cc_start: 0.7204 (m-80) cc_final: 0.6937 (m-80) REVERT: A 155 HIS cc_start: 0.4232 (OUTLIER) cc_final: 0.3670 (m90) REVERT: B 47 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.4759 (mpt) REVERT: B 138 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6405 (tm-30) REVERT: B 246 MET cc_start: 0.7943 (mmt) cc_final: 0.7576 (mmp) REVERT: B 299 ARG cc_start: 0.5895 (ptp-110) cc_final: 0.4825 (tpt170) REVERT: B 328 SER cc_start: 0.7476 (t) cc_final: 0.7200 (p) REVERT: B 344 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6195 (tp30) REVERT: C 313 ASP cc_start: 0.7791 (p0) cc_final: 0.5989 (t0) REVERT: D 41 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7228 (t0) REVERT: D 145 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7371 (mt) REVERT: D 176 LYS cc_start: 0.7143 (tttt) cc_final: 0.6630 (tptp) REVERT: D 186 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7431 (mtt) REVERT: D 359 LYS cc_start: 0.5701 (mptt) cc_final: 0.4335 (ptmt) REVERT: E 102 ASP cc_start: 0.4497 (m-30) cc_final: 0.3762 (t0) REVERT: E 151 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7404 (tp) outliers start: 45 outliers final: 24 residues processed: 206 average time/residue: 0.2355 time to fit residues: 70.7155 Evaluate side-chains 192 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.0770 chunk 13 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 0.0000 overall best weight: 0.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS B 108 ASN B 149 HIS C 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.200663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173575 restraints weight = 15217.015| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.98 r_work: 0.4054 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11986 Z= 0.181 Angle : 0.560 6.685 16266 Z= 0.292 Chirality : 0.044 0.177 1785 Planarity : 0.004 0.059 2070 Dihedral : 10.474 71.630 1825 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.29 % Allowed : 17.64 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1440 helix: 0.64 (0.19), residues: 698 sheet: 0.29 (0.38), residues: 182 loop : -0.02 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 203 HIS 0.006 0.001 HIS A 124 PHE 0.021 0.001 PHE A 357 TYR 0.021 0.001 TYR D 224 ARG 0.005 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6033 (mtt) cc_final: 0.5824 (mtp) REVERT: A 153 PHE cc_start: 0.7040 (m-80) cc_final: 0.6788 (m-80) REVERT: A 155 HIS cc_start: 0.4213 (OUTLIER) cc_final: 0.3721 (m90) REVERT: B 47 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.4253 (mpt) REVERT: B 145 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7119 (mm) REVERT: B 246 MET cc_start: 0.7928 (mmt) cc_final: 0.7691 (mmp) REVERT: B 328 SER cc_start: 0.7431 (t) cc_final: 0.7181 (p) REVERT: B 344 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6004 (tp30) REVERT: C 313 ASP cc_start: 0.7736 (p0) cc_final: 0.5832 (t0) REVERT: D 39 ASP cc_start: 0.6456 (OUTLIER) cc_final: 0.6239 (m-30) REVERT: D 41 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7210 (t0) REVERT: D 145 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7355 (mt) REVERT: D 176 LYS cc_start: 0.7022 (tttt) cc_final: 0.6405 (tptp) REVERT: D 186 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7320 (mtt) REVERT: E 102 ASP cc_start: 0.4684 (m-30) cc_final: 0.3852 (t0) REVERT: E 151 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7353 (tp) outliers start: 41 outliers final: 19 residues processed: 206 average time/residue: 0.2331 time to fit residues: 70.2268 Evaluate side-chains 192 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 0.0060 chunk 69 optimal weight: 1.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS B 108 ASN D 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.195358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.167527 restraints weight = 15269.696| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.00 r_work: 0.3992 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11986 Z= 0.294 Angle : 0.622 6.762 16266 Z= 0.326 Chirality : 0.046 0.240 1785 Planarity : 0.005 0.059 2070 Dihedral : 10.045 73.285 1825 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.05 % Allowed : 18.04 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1440 helix: 0.47 (0.19), residues: 699 sheet: 0.26 (0.38), residues: 188 loop : -0.14 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 203 HIS 0.008 0.001 HIS A 124 PHE 0.017 0.002 PHE A 120 TYR 0.014 0.002 TYR A 224 ARG 0.005 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4256 (OUTLIER) cc_final: 0.3682 (m90) REVERT: B 47 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.4142 (mpt) REVERT: B 145 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7203 (mm) REVERT: B 246 MET cc_start: 0.7991 (mmt) cc_final: 0.7686 (mmp) REVERT: B 328 SER cc_start: 0.7491 (t) cc_final: 0.7222 (p) REVERT: B 344 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5896 (tp30) REVERT: C 313 ASP cc_start: 0.7848 (p0) cc_final: 0.5762 (t0) REVERT: D 41 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7243 (t0) REVERT: D 145 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7505 (mt) REVERT: D 176 LYS cc_start: 0.7153 (tttt) cc_final: 0.6511 (tptp) REVERT: D 186 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7312 (mtt) REVERT: E 102 ASP cc_start: 0.4610 (m-30) cc_final: 0.3792 (t0) REVERT: E 151 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7304 (tp) outliers start: 38 outliers final: 18 residues processed: 193 average time/residue: 0.2346 time to fit residues: 66.0964 Evaluate side-chains 182 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.197501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.171590 restraints weight = 15250.515| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.91 r_work: 0.4041 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11986 Z= 0.199 Angle : 0.554 6.837 16266 Z= 0.290 Chirality : 0.044 0.171 1785 Planarity : 0.005 0.061 2070 Dihedral : 9.320 72.121 1821 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.73 % Allowed : 18.93 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1440 helix: 0.58 (0.19), residues: 701 sheet: 0.26 (0.39), residues: 182 loop : -0.11 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 203 HIS 0.004 0.001 HIS C 290 PHE 0.015 0.001 PHE A 120 TYR 0.014 0.001 TYR D 224 ARG 0.014 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6735 (mmt) cc_final: 0.6332 (mmm) REVERT: A 155 HIS cc_start: 0.4313 (OUTLIER) cc_final: 0.3756 (m90) REVERT: B 47 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.4110 (mpt) REVERT: B 145 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7184 (mm) REVERT: B 246 MET cc_start: 0.7907 (mmt) cc_final: 0.7618 (mmp) REVERT: B 328 SER cc_start: 0.7506 (t) cc_final: 0.7276 (p) REVERT: B 344 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5729 (tp30) REVERT: C 116 ASP cc_start: 0.7469 (m-30) cc_final: 0.7211 (m-30) REVERT: C 313 ASP cc_start: 0.7822 (p0) cc_final: 0.5898 (t0) REVERT: D 41 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7232 (t0) REVERT: D 145 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7475 (mt) REVERT: D 176 LYS cc_start: 0.7031 (tttt) cc_final: 0.6513 (tptp) REVERT: D 186 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7226 (mtt) REVERT: E 102 ASP cc_start: 0.4763 (m-30) cc_final: 0.3798 (t0) REVERT: E 151 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7316 (tp) outliers start: 34 outliers final: 20 residues processed: 194 average time/residue: 0.2297 time to fit residues: 65.4225 Evaluate side-chains 187 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 135 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.198191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171076 restraints weight = 15526.721| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.99 r_work: 0.4033 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11986 Z= 0.213 Angle : 0.562 9.513 16266 Z= 0.294 Chirality : 0.044 0.150 1785 Planarity : 0.004 0.052 2070 Dihedral : 9.069 72.733 1821 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.97 % Allowed : 19.25 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1440 helix: 0.61 (0.19), residues: 700 sheet: 0.31 (0.39), residues: 180 loop : -0.07 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 203 HIS 0.004 0.001 HIS D 124 PHE 0.015 0.001 PHE A 120 TYR 0.016 0.001 TYR D 224 ARG 0.003 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6639 (mmt) cc_final: 0.6367 (mmm) REVERT: A 155 HIS cc_start: 0.4328 (OUTLIER) cc_final: 0.3752 (m90) REVERT: B 47 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.4038 (mpt) REVERT: B 145 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7183 (mm) REVERT: B 246 MET cc_start: 0.7931 (mmt) cc_final: 0.7630 (mmp) REVERT: B 328 SER cc_start: 0.7513 (t) cc_final: 0.7272 (p) REVERT: B 344 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5655 (tp30) REVERT: C 116 ASP cc_start: 0.7474 (m-30) cc_final: 0.7202 (m-30) REVERT: C 313 ASP cc_start: 0.7883 (p0) cc_final: 0.5927 (t0) REVERT: D 41 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7222 (t0) REVERT: D 145 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7517 (mt) REVERT: D 176 LYS cc_start: 0.7029 (tttt) cc_final: 0.6498 (tptp) REVERT: D 186 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7233 (mtt) REVERT: E 60 HIS cc_start: 0.5834 (OUTLIER) cc_final: 0.4350 (t-90) REVERT: E 102 ASP cc_start: 0.4770 (m-30) cc_final: 0.3789 (t0) REVERT: E 151 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7344 (tp) outliers start: 37 outliers final: 26 residues processed: 188 average time/residue: 0.2291 time to fit residues: 63.1739 Evaluate side-chains 191 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.187827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.163988 restraints weight = 15458.696| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.84 r_work: 0.3913 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11986 Z= 0.310 Angle : 0.632 10.525 16266 Z= 0.331 Chirality : 0.046 0.155 1785 Planarity : 0.005 0.058 2070 Dihedral : 9.196 73.965 1821 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.29 % Allowed : 19.33 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1440 helix: 0.41 (0.19), residues: 700 sheet: 0.14 (0.39), residues: 185 loop : -0.29 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 203 HIS 0.007 0.002 HIS D 124 PHE 0.016 0.002 PHE A 120 TYR 0.017 0.002 TYR D 224 ARG 0.006 0.001 ARG D 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.201 Fit side-chains REVERT: A 155 HIS cc_start: 0.4390 (OUTLIER) cc_final: 0.3751 (m90) REVERT: B 47 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.3828 (mpt) REVERT: B 145 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7166 (mm) REVERT: B 246 MET cc_start: 0.8006 (mmt) cc_final: 0.7613 (mmp) REVERT: B 328 SER cc_start: 0.7426 (t) cc_final: 0.7168 (p) REVERT: B 344 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5778 (tp30) REVERT: C 116 ASP cc_start: 0.7562 (m-30) cc_final: 0.7335 (m-30) REVERT: C 313 ASP cc_start: 0.7948 (p0) cc_final: 0.5901 (t0) REVERT: D 41 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7204 (t0) REVERT: D 145 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7545 (mt) REVERT: D 163 ARG cc_start: 0.6739 (mtt180) cc_final: 0.6112 (mtt-85) REVERT: D 176 LYS cc_start: 0.7165 (tttt) cc_final: 0.6484 (tptp) REVERT: D 186 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7226 (mtt) REVERT: E 60 HIS cc_start: 0.5571 (OUTLIER) cc_final: 0.4089 (t-90) REVERT: E 102 ASP cc_start: 0.4663 (m-30) cc_final: 0.3633 (t0) REVERT: E 151 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7386 (tp) outliers start: 41 outliers final: 23 residues processed: 186 average time/residue: 0.2457 time to fit residues: 65.9205 Evaluate side-chains 183 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.186991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.163181 restraints weight = 15413.820| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.82 r_work: 0.3882 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11986 Z= 0.325 Angle : 0.649 8.824 16266 Z= 0.340 Chirality : 0.047 0.191 1785 Planarity : 0.005 0.060 2070 Dihedral : 9.291 73.885 1821 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 19.57 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1440 helix: 0.29 (0.19), residues: 700 sheet: 0.01 (0.38), residues: 185 loop : -0.46 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 203 HIS 0.006 0.001 HIS B 250 PHE 0.015 0.002 PHE A 120 TYR 0.018 0.002 TYR D 224 ARG 0.005 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.277 Fit side-chains REVERT: A 155 HIS cc_start: 0.4422 (OUTLIER) cc_final: 0.3788 (m90) REVERT: B 47 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.3777 (mpt) REVERT: B 115 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5602 (ttm-80) REVERT: B 138 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6626 (pt0) REVERT: B 145 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7180 (mm) REVERT: B 246 MET cc_start: 0.8029 (mmt) cc_final: 0.7713 (mmp) REVERT: B 328 SER cc_start: 0.7468 (t) cc_final: 0.7213 (p) REVERT: B 344 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.5848 (tp30) REVERT: C 313 ASP cc_start: 0.7951 (p0) cc_final: 0.5880 (t0) REVERT: D 41 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7244 (t0) REVERT: D 145 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7495 (mm) REVERT: D 163 ARG cc_start: 0.6808 (mtt180) cc_final: 0.6174 (mtt-85) REVERT: D 176 LYS cc_start: 0.7175 (tttt) cc_final: 0.6491 (tptp) REVERT: D 186 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7293 (mtt) REVERT: E 60 HIS cc_start: 0.5727 (OUTLIER) cc_final: 0.4211 (t-90) REVERT: E 102 ASP cc_start: 0.4732 (m-30) cc_final: 0.3780 (t0) REVERT: E 128 MET cc_start: 0.2642 (tmm) cc_final: 0.2434 (mmp) outliers start: 38 outliers final: 26 residues processed: 186 average time/residue: 0.2506 time to fit residues: 66.7960 Evaluate side-chains 188 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 0.6980 chunk 98 optimal weight: 0.0170 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.191245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168587 restraints weight = 15173.353| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.72 r_work: 0.3937 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11986 Z= 0.190 Angle : 0.571 8.689 16266 Z= 0.300 Chirality : 0.044 0.158 1785 Planarity : 0.005 0.055 2070 Dihedral : 8.972 72.364 1821 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 20.21 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1440 helix: 0.52 (0.19), residues: 700 sheet: 0.10 (0.39), residues: 179 loop : -0.32 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 203 HIS 0.004 0.001 HIS C 124 PHE 0.013 0.001 PHE A 120 TYR 0.021 0.001 TYR D 224 ARG 0.006 0.000 ARG D 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.6478 (mmt) cc_final: 0.6248 (tpt) REVERT: A 155 HIS cc_start: 0.4423 (OUTLIER) cc_final: 0.3843 (m90) REVERT: B 47 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.3694 (mpt) REVERT: B 145 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7153 (mm) REVERT: B 246 MET cc_start: 0.7943 (mmt) cc_final: 0.7696 (mmp) REVERT: B 299 ARG cc_start: 0.7029 (ttp-170) cc_final: 0.6766 (ptt180) REVERT: B 328 SER cc_start: 0.7476 (t) cc_final: 0.7231 (p) REVERT: B 344 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5598 (tp30) REVERT: C 116 ASP cc_start: 0.7398 (m-30) cc_final: 0.7177 (m-30) REVERT: C 313 ASP cc_start: 0.7852 (p0) cc_final: 0.5832 (t0) REVERT: D 41 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7164 (t0) REVERT: D 145 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7524 (mt) REVERT: D 163 ARG cc_start: 0.6728 (mtt180) cc_final: 0.6103 (mtt-85) REVERT: D 176 LYS cc_start: 0.7034 (tttt) cc_final: 0.6460 (tptp) REVERT: D 186 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7242 (mtt) REVERT: E 60 HIS cc_start: 0.5874 (OUTLIER) cc_final: 0.4159 (t-90) REVERT: E 102 ASP cc_start: 0.4841 (m-30) cc_final: 0.3780 (t0) outliers start: 31 outliers final: 21 residues processed: 178 average time/residue: 0.2456 time to fit residues: 62.9175 Evaluate side-chains 179 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 0.0270 chunk 115 optimal weight: 7.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.192790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169413 restraints weight = 15214.886| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.78 r_work: 0.3946 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11986 Z= 0.176 Angle : 0.552 8.942 16266 Z= 0.290 Chirality : 0.043 0.150 1785 Planarity : 0.004 0.051 2070 Dihedral : 8.776 72.007 1821 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.33 % Allowed : 20.45 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1440 helix: 0.66 (0.20), residues: 700 sheet: 0.19 (0.39), residues: 179 loop : -0.24 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 203 HIS 0.004 0.001 HIS C 124 PHE 0.013 0.001 PHE A 120 TYR 0.030 0.001 TYR D 224 ARG 0.009 0.000 ARG B 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6596.80 seconds wall clock time: 119 minutes 8.11 seconds (7148.11 seconds total)